A new approach to compute accurate velocity of meteors
NASA Astrophysics Data System (ADS)
Egal, Auriane; Gural, Peter; Vaubaillon, Jeremie; Colas, Francois; Thuillot, William
2016-10-01
The CABERNET project was designed to push the limits of meteoroid orbit measurements by improving the determination of the meteors' velocities. Indeed, despite of the development of the cameras networks dedicated to the observation of meteors, there is still an important discrepancy between the measured orbits of meteoroids computed and the theoretical results. The gap between the observed and theoretic semi-major axis of the orbits is especially significant; an accurate determination of the orbits of meteoroids therefore largely depends on the computation of the pre-atmospheric velocities. It is then imperative to dig out how to increase the precision of the measurements of the velocity.In this work, we perform an analysis of different methods currently used to compute the velocities and trajectories of the meteors. They are based on the intersecting planes method developed by Ceplecha (1987), the least squares method of Borovicka (1990), and the multi-parameter fitting (MPF) method published by Gural (2012).In order to objectively compare the performances of these techniques, we have simulated realistic meteors ('fakeors') reproducing the different error measurements of many cameras networks. Some fakeors are built following the propagation models studied by Gural (2012), and others created by numerical integrations using the Borovicka et al. 2007 model. Different optimization techniques have also been investigated in order to pick the most suitable one to solve the MPF, and the influence of the geometry of the trajectory on the result is also presented.We will present here the results of an improved implementation of the multi-parameter fitting that allow an accurate orbit computation of meteors with CABERNET. The comparison of different velocities computation seems to show that if the MPF is by far the best method to solve the trajectory and the velocity of a meteor, the ill-conditioning of the costs functions used can lead to large estimate errors for noisy
Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew
2014-03-20
Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modeling flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.
Schirle, M; Weinschenk, T; Stevanović, S
2001-11-01
The identification of T cell epitopes from immunologically relevant antigens remains a critical step in the development of vaccines and methods for monitoring of T cell responses. This review presents an overview of strategies that employ computer algorithms for the selection of candidate peptides from defined proteins and subsequent verification of their in vivo relevance by experimental approaches. Several computer algorithms are currently being used for epitope prediction of various major histocompatibility complex (MHC) class I and II molecules, based either on the analysis of natural MHC ligands or on the binding properties of synthetic peptides. Moreover, the analysis of proteasomal digests of peptides and whole proteins has led to the development of algorithms for the prediction of proteasomal cleavages. In order to verify the generation of the predicted peptides during antigen processing in vivo as well as their immunogenic potential, several experimental approaches have been pursued in the recent past. Mass spectrometry-based bioanalytical approaches have been used specifically to detect predicted peptides among isolated natural ligands. Other strategies employ various methods for the stimulation of primary T cell responses against the predicted peptides and subsequent testing of the recognition pattern towards target cells that express the antigen.
Chen, Liao Y
2015-04-14
Computing the free energy of binding a ligand to a protein is a difficult task of essential importance for which purpose various theoretical/computational approaches have been pursued. In this paper, we develop a hybrid steered molecular dynamics (hSMD) method capable of resolving one ligand–protein complex within a few wall-clock days with high enough accuracy to compare with the experimental data. This hSMD approach is based on the relationship between the binding affinity and the potential of mean force (PMF) in the established literature. It involves simultaneously steering n (n = 1, 2, 3, ...) centers of mass of n selected segments of the ligand using n springs of infinite stiffness. Steering the ligand from a single initial state chosen from the bound state ensemble to the corresponding dissociated state, disallowing any fluctuations of the pulling centers along the way, one can determine a 3n-dimensional PMF curve connecting the two states by sampling a small number of forward and reverse pulling paths. This PMF constitutes a large but not the sole contribution to the binding free energy. Two other contributors are (1) the partial partition function containing the equilibrium fluctuations of the ligand at the binding site and the deviation of the initial state from the PMF minimum and (2) the partial partition function containing rotation and fluctuations of the ligand around one of the pulling centers that is fixed at a position far from the protein. We implement this hSMD approach for two ligand–protein complexes whose structures were determined and whose binding affinities were measured experimentally: caprylic acid binding to bovine β-lactoglobulin and glutathione binding to Schistosoma japonicum glutathione S-transferase tyrosine 7 to phenylalanine mutant. Our computed binding affinities agree with the experimental data within a factor of 1.5. The total time of computation for these two all-atom model systems (consisting of 96K and 114K atoms
Accurate method for computing correlated color temperature.
Li, Changjun; Cui, Guihua; Melgosa, Manuel; Ruan, Xiukai; Zhang, Yaoju; Ma, Long; Xiao, Kaida; Luo, M Ronnier
2016-06-27
For the correlated color temperature (CCT) of a light source to be estimated, a nonlinear optimization problem must be solved. In all previous methods available to compute CCT, the objective function has only been approximated, and their predictions have achieved limited accuracy. For example, different unacceptable CCT values have been predicted for light sources located on the same isotemperature line. In this paper, we propose to compute CCT using the Newton method, which requires the first and second derivatives of the objective function. Following the current recommendation by the International Commission on Illumination (CIE) for the computation of tristimulus values (summations at 1 nm steps from 360 nm to 830 nm), the objective function and its first and second derivatives are explicitly given and used in our computations. Comprehensive tests demonstrate that the proposed method, together with an initial estimation of CCT using Robertson's method [J. Opt. Soc. Am. 58, 1528-1535 (1968)], gives highly accurate predictions below 0.0012 K for light sources with CCTs ranging from 500 K to 10^{6} K.
Kang, Runhua; Lai, Wenzhen; Yao, Jiannian; Shaik, Sason; Chen, Hui
2012-09-11
To improve the accuracy of local coupled cluster (LCC) methods in computing activation energies, we propose herein a new computational scheme. Its applications to various types of late-transition-metal-catalyzed reactions involving Au, Pt, and Ir indicate that the new corrective approach for LCC methods can downsize the mean unsigned deviation and maximum deviation, from the CCSD(T)/CBS reference, to about 0.3 and 0.9 kcal/mol. Using this method, we also calibrated the performance of popular density functionals, with respect to the same test set of reactions. It is concluded that the best functional is the general-purpose double hybrid functional B2GP-PLYP. Other well-performing functionals include the "kinetic" functionals M06-2X and BMK, which have a large percentage of HF exchange, and general-purpose functionals like PBE0 and wB97X. Comparatively, general-purpose functionals like PBE0 and TPSSh perform much better than the tested "kinetic" functionals for Pt-/Ir-catalyzed reactions, while the opposite is true for Au-catalyzed reactions. In contrast, wB97X performs more uniformly in these two classes of reactions. These findings hint that even within the scope of late transition metals, different types of reactions may require different types of optimal DFT methods. Empirical dispersion correction of DFT was found to have a small or no effect on the studied reactions barriers.
Accurate paleointensities - the multi-method approach
NASA Astrophysics Data System (ADS)
de Groot, Lennart
2016-04-01
The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.
Accurate atom-mapping computation for biochemical reactions.
Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D
2012-11-26
The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.
ERIC Educational Resources Information Center
Harbusch, Karin; Itsova, Gergana; Koch, Ulrich; Kuhner, Christine
2009-01-01
We built a natural language processing (NLP) system implementing a "virtual writing conference" for elementary-school children, with German as the target language. Currently, state-of-the-art computer support for writing tasks is restricted to multiple-choice questions or quizzes because automatic parsing of the often ambiguous and fragmentary…
Photoacoustic computed tomography without accurate ultrasonic transducer responses
NASA Astrophysics Data System (ADS)
Sheng, Qiwei; Wang, Kun; Xia, Jun; Zhu, Liren; Wang, Lihong V.; Anastasio, Mark A.
2015-03-01
Conventional photoacoustic computed tomography (PACT) image reconstruction methods assume that the object and surrounding medium are described by a constant speed-of-sound (SOS) value. In order to accurately recover fine structures, SOS heterogeneities should be quantified and compensated for during PACT reconstruction. To address this problem, several groups have proposed hybrid systems that combine PACT with ultrasound computed tomography (USCT). In such systems, a SOS map is reconstructed first via USCT. Consequently, this SOS map is employed to inform the PACT reconstruction method. Additionally, the SOS map can provide structural information regarding tissue, which is complementary to the functional information from the PACT image. We propose a paradigm shift in the way that images are reconstructed in hybrid PACT-USCT imaging. Inspired by our observation that information about the SOS distribution is encoded in PACT measurements, we propose to jointly reconstruct the absorbed optical energy density and SOS distributions from a combined set of USCT and PACT measurements, thereby reducing the two reconstruction problems into one. This innovative approach has several advantages over conventional approaches in which PACT and USCT images are reconstructed independently: (1) Variations in the SOS will automatically be accounted for, optimizing PACT image quality; (2) The reconstructed PACT and USCT images will possess minimal systematic artifacts because errors in the imaging models will be optimally balanced during the joint reconstruction; (3) Due to the exploitation of information regarding the SOS distribution in the full-view PACT data, our approach will permit high-resolution reconstruction of the SOS distribution from sparse array data.
Preparing Rapid, Accurate Construction Cost Estimates with a Personal Computer.
ERIC Educational Resources Information Center
Gerstel, Sanford M.
1986-01-01
An inexpensive and rapid method for preparing accurate cost estimates of construction projects in a university setting, using a personal computer, purchased software, and one estimator, is described. The case against defined estimates, the rapid estimating system, and adjusting standard unit costs are discussed. (MLW)
Efficient and accurate computation of the incomplete Airy functions
NASA Technical Reports Server (NTRS)
Constantinides, E. D.; Marhefka, R. J.
1993-01-01
The incomplete Airy integrals serve as canonical functions for the uniform ray optical solutions to several high-frequency scattering and diffraction problems that involve a class of integrals characterized by two stationary points that are arbitrarily close to one another or to an integration endpoint. Integrals with such analytical properties describe transition region phenomena associated with composite shadow boundaries. An efficient and accurate method for computing the incomplete Airy functions would make the solutions to such problems useful for engineering purposes. In this paper a convergent series solution for the incomplete Airy functions is derived. Asymptotic expansions involving several terms are also developed and serve as large argument approximations. The combination of the series solution with the asymptotic formulae provides for an efficient and accurate computation of the incomplete Airy functions. Validation of accuracy is accomplished using direct numerical integration data.
Accurate and fast computation of transmission cross coefficients
NASA Astrophysics Data System (ADS)
Apostol, Štefan; Hurley, Paul; Ionescu, Radu-Cristian
2015-03-01
Precise and fast computation of aerial images are essential. Typical lithographic simulators employ a Köhler illumination system for which aerial imagery is obtained using a large number of Transmission Cross Coefficients (TCCs). These are generally computed by a slow numerical evaluation of a double integral. We review the general framework in which the 2D imagery is solved and then propose a fast and accurate method to obtain the TCCs. We acquire analytical solutions and thus avoid the complexity-accuracy trade-off encountered with numerical integration. Compared to other analytical integration methods, the one presented is faster, more general and more tractable.
An Accurate and Efficient Method of Computing Differential Seismograms
NASA Astrophysics Data System (ADS)
Hu, S.; Zhu, L.
2013-12-01
Inversion of seismic waveforms for Earth structure usually requires computing partial derivatives of seismograms with respect to velocity model parameters. We developed an accurate and efficient method to calculate differential seismograms for multi-layered elastic media, based on the Thompson-Haskell propagator matrix technique. We first derived the partial derivatives of the Haskell matrix and its compound matrix respect to the layer parameters (P wave velocity, shear wave velocity and density). We then derived the partial derivatives of surface displacement kernels in the frequency-wavenumber domain. The differential seismograms are obtained by using the frequency-wavenumber double integration method. The implementation is computationally efficient and the total computing time is proportional to the time of computing the seismogram itself, i.e., independent of the number of layers in the model. We verified the correctness of results by comparing with differential seismograms computed using the finite differences method. Our results are more accurate because of the analytical nature of the derived partial derivatives.
Computational Time-Accurate Body Movement: Methodology, Validation, and Application
1995-10-01
used that had a leading-edge sweep angle of 45 deg and a NACA 64A010 symmetrical airfoil section. A cross section of the pylon is a symmetrical...25 2. Information Flow for the Time-Accurate Store Trajectory Prediction Process . . . . . . . . . 26 3. Pitch Rates for NACA -0012 Airfoil...section are comparisons of the computational results to data for a NACA -0012 airfoil following a predefined pitching motion. Validation of the
Accurate Langevin approaches to simulate Markovian channel dynamics
NASA Astrophysics Data System (ADS)
Huang, Yandong; Rüdiger, Sten; Shuai, Jianwei
2015-12-01
The stochasticity of ion-channels dynamic is significant for physiological processes on neuronal cell membranes. Microscopic simulations of the ion-channel gating with Markov chains can be considered to be an accurate standard. However, such Markovian simulations are computationally demanding for membrane areas of physiologically relevant sizes, which makes the noise-approximating or Langevin equation methods advantageous in many cases. In this review, we discuss the Langevin-like approaches, including the channel-based and simplified subunit-based stochastic differential equations proposed by Fox and Lu, and the effective Langevin approaches in which colored noise is added to deterministic differential equations. In the framework of Fox and Lu’s classical models, several variants of numerical algorithms, which have been recently developed to improve accuracy as well as efficiency, are also discussed. Through the comparison of different simulation algorithms of ion-channel noise with the standard Markovian simulation, we aim to reveal the extent to which the existing Langevin-like methods approximate results using Markovian methods. Open questions for future studies are also discussed.
Direct computation of parameters for accurate polarizable force fields
Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.
2014-11-21
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
An Accurate and Dynamic Computer Graphics Muscle Model
NASA Technical Reports Server (NTRS)
Levine, David Asher
1997-01-01
A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.
Accurate computation of Zernike moments in polar coordinates.
Xin, Yongqing; Pawlak, Miroslaw; Liao, Simon
2007-02-01
An algorithm for high-precision numerical computation of Zernike moments is presented. The algorithm, based on the introduced polar pixel tiling scheme, does not exhibit the geometric error and numerical integration error which are inherent in conventional methods based on Cartesian coordinates. This yields a dramatic improvement of the Zernike moments accuracy in terms of their reconstruction and invariance properties. The introduced image tiling requires an interpolation algorithm which turns out to be of the second order importance compared to the discretization error. Various comparisons are made between the accuracy of the proposed method and that of commonly used techniques. The results reveal the great advantage of our approach.
Madebene, Bruno; Ulusoy, Inga; Mancera, Luis; Scribano, Yohann; Chulkov, Sergey
2011-01-01
Summary We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters. PMID:22003450
Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics
NASA Technical Reports Server (NTRS)
Goodrich, John W.; Dyson, Rodger W.
1999-01-01
The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that
Accurate Anharmonic IR Spectra from Integrated Cc/dft Approach
NASA Astrophysics Data System (ADS)
Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Carnimeo, Ivan; Puzzarini, Cristina
2014-06-01
The recent implementation of the computation of infrared (IR) intensities beyond the double harmonic approximation [1] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Contrary to common beliefs, second-order perturbation theory is able to deliver results of high accuracy provided that anharmonic resonances are properly managed [1,2]. It has been already shown for several small closed- and open shell molecular systems that the differences between coupled cluster (CC) and DFT anharmonic wavenumbers are mainly due to the harmonic terms, paving the route to introduce effective yet accurate hybrid CC/DFT schemes [2]. In this work we present that hybrid CC/DFT models can be applied also to the IR intensities leading to the simulation of highly accurate fully anharmonic IR spectra for medium-size molecules, including ones of atmospheric interest, showing in all cases good agreement with experiment even in the spectral ranges where non-fundamental transitions are predominant[3]. [1] J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012) [2] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 16, 1759-1787 (2014) [3] I. Carnimeo, C. Puzzarini, N. Tasinato, P. Stoppa, A. P. Charmet, M. Biczysko, C. Cappelli and V. Barone, J. Chem. Phys., 139, 074310 (2013)
Computational approaches to computational aero-acoustics
NASA Technical Reports Server (NTRS)
Hardin, Jay C.
1996-01-01
The various techniques by which the goal of computational aeroacoustics (the calculation and noise prediction of a fluctuating fluid flow) may be achieved are reviewed. The governing equations for compressible fluid flow are presented. The direct numerical simulation approach is shown to be computationally intensive for high Reynolds number viscous flows. Therefore, other approaches, such as the acoustic analogy, vortex models and various perturbation techniques that aim to break the analysis into a viscous part and an acoustic part are presented. The choice of the approach is shown to be problem dependent.
Computational approaches to vision
NASA Technical Reports Server (NTRS)
Barrow, H. G.; Tenenbaum, J. M.
1986-01-01
Vision is examined in terms of a computational process, and the competence, structure, and control of computer vision systems are analyzed. Theoretical and experimental data on the formation of a computer vision system are discussed. Consideration is given to early vision, the recovery of intrinsic surface characteristics, higher levels of interpretation, and system integration and control. A computational visual processing model is proposed and its architecture and operation are described. Examples of state-of-the-art vision systems, which include some of the levels of representation and processing mechanisms, are presented.
Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L
2016-01-01
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.
Towards accurate quantum simulations of large systems with small computers
NASA Astrophysics Data System (ADS)
Yang, Yonggang
2017-01-01
Numerical simulations are important for many systems. In particular, various standard computer programs have been developed for solving the quantum Schrödinger equations. However, the accuracy of these calculations is limited by computer capabilities. In this work, an iterative method is introduced to enhance the accuracy of these numerical calculations, which is otherwise prohibitive by conventional methods. The method is easily implementable and general for many systems.
Towards accurate quantum simulations of large systems with small computers.
Yang, Yonggang
2017-01-24
Numerical simulations are important for many systems. In particular, various standard computer programs have been developed for solving the quantum Schrödinger equations. However, the accuracy of these calculations is limited by computer capabilities. In this work, an iterative method is introduced to enhance the accuracy of these numerical calculations, which is otherwise prohibitive by conventional methods. The method is easily implementable and general for many systems.
Towards accurate quantum simulations of large systems with small computers
Yang, Yonggang
2017-01-01
Numerical simulations are important for many systems. In particular, various standard computer programs have been developed for solving the quantum Schrödinger equations. However, the accuracy of these calculations is limited by computer capabilities. In this work, an iterative method is introduced to enhance the accuracy of these numerical calculations, which is otherwise prohibitive by conventional methods. The method is easily implementable and general for many systems. PMID:28117366
Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.
2015-01-01
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739
Passeri, A; Formiconi, A R; De Cristofaro, M T; Pupi, A; Meldolesi, U
1997-04-01
It is well known that the quantitative potential of emission computed tomography (ECT) relies on the ability to compensate for resolution, attenuation and scatter effects. Reconstruction algorithms which are able to take these effects into account are highly demanding in terms of computing resources. The reported work aimed to investigate the use of a parallel high-performance computing platform for ECT reconstruction taking into account an accurate model of the acquisition of single-photon emission tomographic (SPET) data. An iterative algorithm with an accurate model of the variable system response was ported on the MIMD (Multiple Instruction Multiple Data) parallel architecture of a 64-node Cray T3D massively parallel computer. The system was organized to make it easily accessible even from low-cost PC-based workstations through standard TCP/IP networking. A complete brain study of 30 (64x64) slices could be reconstructed from a set of 90 (64x64) projections with ten iterations of the conjugate gradients algorithm in 9 s, corresponding to an actual speed-up factor of 135. This work demonstrated the possibility of exploiting remote high-performance computing and networking resources from hospital sites by means of low-cost workstations using standard communication protocols without particular problems for routine use. The achievable speed-up factors allow the assessment of the clinical benefit of advanced reconstruction techniques which require a heavy computational burden for the compensation effects such as variable spatial resolution, scatter and attenuation. The possibility of using the same software on the same hardware platform with data acquired in different laboratories with various kinds of SPET instrumentation is appealing for software quality control and for the evaluation of the clinical impact of the reconstruction methods.
NASA Astrophysics Data System (ADS)
Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi
2015-02-01
With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.
NASA Technical Reports Server (NTRS)
Tamma, Kumar K.; Railkar, Sudhir B.
1988-01-01
This paper represents an attempt to apply extensions of a hybrid transfinite element computational approach for accurately predicting thermoelastic stress waves. The applicability of the present formulations for capturing the thermal stress waves induced by boundary heating for the well known Danilovskaya problems is demonstrated. A unique feature of the proposed formulations for applicability to the Danilovskaya problem of thermal stress waves in elastic solids lies in the hybrid nature of the unified formulations and the development of special purpose transfinite elements in conjunction with the classical Galerkin techniques and transformation concepts. Numerical test cases validate the applicability and superior capability to capture the thermal stress waves induced due to boundary heating.
Mapping methods for computationally efficient and accurate structural reliability
NASA Technical Reports Server (NTRS)
Shiao, Michael C.; Chamis, Christos C.
1992-01-01
Mapping methods are developed to improve the accuracy and efficiency of probabilistic structural analyses with coarse finite element meshes. The mapping methods consist of: (1) deterministic structural analyses with fine (convergent) finite element meshes, (2) probabilistic structural analyses with coarse finite element meshes, (3) the relationship between the probabilistic structural responses from the coarse and fine finite element meshes, and (4) a probabilistic mapping. The results show that the scatter of the probabilistic structural responses and structural reliability can be accurately predicted using a coarse finite element model with proper mapping methods. Therefore, large structures can be analyzed probabilistically using finite element methods.
Approaches for the accurate definition of geological time boundaries
NASA Astrophysics Data System (ADS)
Schaltegger, Urs; Baresel, Björn; Ovtcharova, Maria; Goudemand, Nicolas; Bucher, Hugo
2015-04-01
Which strategies lead to the most precise and accurate date of a given geological boundary? Geological units are usually defined by the occurrence of characteristic taxa and hence boundaries between these geological units correspond to dramatic faunal and/or floral turnovers and they are primarily defined using first or last occurrences of index species, or ideally by the separation interval between two consecutive, characteristic associations of fossil taxa. These boundaries need to be defined in a way that enables their worldwide recognition and correlation across different stratigraphic successions, using tools as different as bio-, magneto-, and chemo-stratigraphy, and astrochronology. Sedimentary sequences can be dated in numerical terms by applying high-precision chemical-abrasion, isotope-dilution, thermal-ionization mass spectrometry (CA-ID-TIMS) U-Pb age determination to zircon (ZrSiO4) in intercalated volcanic ashes. But, though volcanic activity is common in geological history, ashes are not necessarily close to the boundary we would like to date precisely and accurately. In addition, U-Pb zircon data sets may be very complex and difficult to interpret in terms of the age of ash deposition. To overcome these difficulties we use a multi-proxy approach we applied to the precise and accurate dating of the Permo-Triassic and Early-Middle Triassic boundaries in South China. a) Dense sampling of ashes across the critical time interval and a sufficiently large number of analysed zircons per ash sample can guarantee the recognition of all system complexities. Geochronological datasets from U-Pb dating of volcanic zircon may indeed combine effects of i) post-crystallization Pb loss from percolation of hydrothermal fluids (even using chemical abrasion), with ii) age dispersion from prolonged residence of earlier crystallized zircon in the magmatic system. As a result, U-Pb dates of individual zircons are both apparently younger and older than the depositional age
Accurate Computation of Divided Differences of the Exponential Function,
1983-06-01
differences are not for arbitrary smooth functions f but for well known analytic functions such as exp. sin and cos. Thus we can exploit their properties in...have a bad name in practice. However in a number of applications the functional form of f is known (e.g. exp) and can be exploited to obtain accurate...n do X =s(1) s(1)=d(i) For j=2.....-1 do11=t, (j) z=Y next j next i SS7 . (Shift back and stop.] ,-tt+77. d(i).-e"d(i), s(i-1)’e~ s(i-i) for i=2
Casing shoe depths accurately and quickly selected with computer assistance
Mattiello, D.; Piantanida, M.; Schenato, A.; Tomada, L. )
1993-10-04
A computer-aided support system for casing design and shoe depth selection improves the reliability of solutions, reduces total project time, and helps reduce costs. This system is part of ADIS (Advanced Drilling Information System), an integrated environment developed by three companies of the ENI group (Agip SpA, Enidata, and Saipem). The ADIS project focuses on the on site planning and control of drilling operations. The first version of the computer-aided support for casing design (Cascade) was experimentally introduced by Agip SpA in July 1991. After several modifications, the system was introduced to field operations in December 1991 and is now used in Agip's district locations and headquarters. The results from the validation process and practical uses indicated it has several pluses: the reliability of the casing shoe depths proposed by the system helps reduce the project errors and improve the economic feasibility of the proposed solutions; the system has helped spread the use of the best engineering practices concerning shoe depth selection and casing design; the Cascade system finds numerous solutions rapidly, thereby reducing project time compared to previous methods of casing design; the system finds or verifies solutions efficiently, allowing the engineer to analyze several alternatives simultaneously rather than to concentrate only on the analysis of a single solution; the system is flexible by means of a user-friendly integration with the other software packages in the ADIS project. The paper describes the design methodology, validation cases, shoe depths, casing design, hardware and software, and results.
Macromolecular Entropy Can Be Accurately Computed from Force.
Hensen, Ulf; Gräter, Frauke; Henchman, Richard H
2014-11-11
A method is presented to evaluate a molecule's entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a β hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The method's accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.
An Approach for the Accurate Measurement of Social Morality Levels
Liu, Haiyan; Chen, Xia; Zhang, Bo
2013-01-01
In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources. Threshold values for the various parameters are obtained through sensitivity analysis; and practical solutions are proposed for reversing declines in social morality levels. The results show that: (1) Population size may accelerate or impede the speed with which immoral behavior comes to determine the overall level of social morality, but it has no effect on the level of social morality itself; (2) The impact of rewards and punishment on social morality levels follows the “5∶1 rewards-to-punishment rule,” which is to say that 5 units of rewards have the same effect as 1 unit of punishment; (3) The abundance of public resources is inversely related to the level of social morality; (4) When the cost of population mobility reaches 10% of the total energy level, immoral behavior begins to be suppressed (i.e. the 1/10 moral cost rule). The research approach and methods presented in this paper successfully address the difficulties involved in measuring social morality levels, and promise extensive application potentials. PMID:24312189
Groundtruth approach to accurate quantitation of fluorescence microarrays
Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J
2000-12-01
To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval
Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman
2015-01-01
The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226
Development of highly accurate approximate scheme for computing the charge transfer integral
NASA Astrophysics Data System (ADS)
Pershin, Anton; Szalay, Péter G.
2015-08-01
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.
Development of highly accurate approximate scheme for computing the charge transfer integral.
Pershin, Anton; Szalay, Péter G
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.
Development of highly accurate approximate scheme for computing the charge transfer integral
Pershin, Anton; Szalay, Péter G.
2015-08-21
The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.
Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images
NASA Technical Reports Server (NTRS)
Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.
1999-01-01
Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.
Kouznetsov, Alexei; Tambasco, Mauro
2011-03-15
Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.
NASA Astrophysics Data System (ADS)
Lee, T. J.; Huang, X.; Schwenke, D. W.
2013-12-01
Over the last decade, it has become apparent that the most effective approach for determining highly accurate rotational and rovibrational line lists for molecules of interest in planetary atmospheres is through a combination of high-resolution laboratory experiments coupled with state-of-the art ab initio quantum chemistry methods. The approach involves computing the most accurate potential energy surface (PES) possible using state-of-the art electronic structure methods, followed by computing rotational and rovibrational energy levels using an exact variational method to solve the nuclear Schrödinger equation. Then, reliable experimental data from high-resolution experiments is used to refine the ab initio PES in order to improve the accuracy of the computed energy levels and transition energies. From the refinement step, we have been able to achieve an accuracy of approximately 0.015 cm-1 for rovibrational transition energies, and even better for purely rotational transitions. This combined 'experiment / theory' approach allows for determination of essentially a complete line list, with hundreds of millions of transitions, and having the transition energies and intensities be highly accurate. Our group has successfully applied this approach to determine highly accurate line lists for NH3 and CO2 (and isotopologues), and very recently for SO2 and isotopologues. Here I will report our latest results for SO2 including all isotopologues. Comparisons to the available data in HITRAN2012 and other available databases will be shown, though we note that our line lists SO2 are significantly more complete than any other databases. Since it is important to span a large temperature range in order to model the spectral signature of exoplanets, we will also demonstrate how the spectra change on going from low temperatures (100 K) to higher temperatures (500 K).
NASA Astrophysics Data System (ADS)
Cary, John R.; Abell, D.; Amundson, J.; Bruhwiler, D. L.; Busby, R.; Carlsson, J. A.; Dimitrov, D. A.; Kashdan, E.; Messmer, P.; Nieter, C.; Smithe, D. N.; Spentzouris, P.; Stoltz, P.; Trines, R. M.; Wang, H.; Werner, G. R.
2006-09-01
As the size and cost of particle accelerators escalate, high-performance computing plays an increasingly important role; optimization through accurate, detailed computermodeling increases performance and reduces costs. But consequently, computer simulations face enormous challenges. Early approximation methods, such as expansions in distance from the design orbit, were unable to supply detailed accurate results, such as in the computation of wake fields in complex cavities. Since the advent of message-passing supercomputers with thousands of processors, earlier approximations are no longer necessary, and it is now possible to compute wake fields, the effects of dampers, and self-consistent dynamics in cavities accurately. In this environment, the focus has shifted towards the development and implementation of algorithms that scale to large numbers of processors. So-called charge-conserving algorithms evolve the electromagnetic fields without the need for any global solves (which are difficult to scale up to many processors). Using cut-cell (or embedded) boundaries, these algorithms can simulate the fields in complex accelerator cavities with curved walls. New implicit algorithms, which are stable for any time-step, conserve charge as well, allowing faster simulation of structures with details small compared to the characteristic wavelength. These algorithmic and computational advances have been implemented in the VORPAL7 Framework, a flexible, object-oriented, massively parallel computational application that allows run-time assembly of algorithms and objects, thus composing an application on the fly.
Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.
ERIC Educational Resources Information Center
Albee, David; Jones, Edward
1989-01-01
Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)
Computational Approaches to Vestibular Research
NASA Technical Reports Server (NTRS)
Ross, Muriel D.; Wade, Charles E. (Technical Monitor)
1994-01-01
The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and
Computer-based personality judgments are more accurate than those made by humans
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-01
Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507
Computer-based personality judgments are more accurate than those made by humans.
Youyou, Wu; Kosinski, Michal; Stillwell, David
2015-01-27
Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.
Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach
Saa, Pedro A.; Nielsen, Lars K.
2016-01-01
Kinetic models are essential to quantitatively understand and predict the behaviour of metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism are inherently difficult to formulate and fit. They have a large number of heterogeneous parameters, are non-linear and have complex interactions. Many powerful fitting strategies are ruled out by the intractability of the likelihood function. Here, we have developed a computational framework capable of fitting feasible and accurate kinetic models using Approximate Bayesian Computation. This framework readily supports advanced modelling features such as model selection and model-based experimental design. We illustrate this approach on the tightly-regulated mammalian methionine cycle. Sampling from the posterior distribution, the proposed framework generated thermodynamically feasible parameter samples that converged on the true values, and displayed remarkable prediction accuracy in several validation tests. Furthermore, a posteriori analysis of the parameter distributions enabled appraisal of the systems properties of the network (e.g., control structure) and key metabolic regulations. Finally, the framework was used to predict missing allosteric interactions. PMID:27417285
Are accurate computations of the 13C' shielding feasible at the DFT level of theory?
Vila, Jorge A; Arnautova, Yelena A; Martin, Osvaldo A; Scheraga, Harold A
2014-02-05
The goal of this study is twofold. First, to investigate the relative influence of the main structural factors affecting the computation of the (13)C' shielding, namely, the conformation of the residue itself and the next nearest-neighbor effects. Second, to determine whether calculation of the (13)C' shielding at the density functional level of theory (DFT), with an accuracy similar to that of the (13)C(α) shielding, is feasible with the existing computational resources. The DFT calculations, carried out for a large number of possible conformations of the tripeptide Ac-GXY-NMe, with different combinations of X and Y residues, enable us to conclude that the accurate computation of the (13)C' shielding for a given residue X depends on the: (i) (ϕ,ψ) backbone torsional angles of X; (ii) side-chain conformation of X; (iii) (ϕ,ψ) torsional angles of Y; and (iv) identity of residue Y. Consequently, DFT-based quantum mechanical calculations of the (13)C' shielding, with all these factors taken into account, are two orders of magnitude more CPU demanding than the computation, with similar accuracy, of the (13)C(α) shielding. Despite not considering the effect of the possible hydrogen bond interaction of the carbonyl oxygen, this work contributes to our general understanding of the main structural factors affecting the accurate computation of the (13)C' shielding in proteins and may spur significant progress in effort to develop new validation methods for protein structures.
NASA Astrophysics Data System (ADS)
Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua
2014-11-01
Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.
Yoshidome, Takashi; Ekimoto, Toru; Matubayasi, Nobuyuki; Harano, Yuichi; Kinoshita, Masahiro; Ikeguchi, Mitsunori
2015-05-07
The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of 〈UUV〉/2 (〈UUV〉 is the ensemble average of the sum of pair interaction energy between solute and water molecule) and the water reorganization term mainly reflecting the excluded volume effect. Since 〈UUV〉 can readily be computed through a MD of the system composed of solute and water, an efficient computation of the latter term leads to a reduction of computational load. We demonstrate that the water reorganization term can quantitatively be calculated using the morphometric approach (MA) which expresses the term as the linear combinations of the four geometric measures of a solute and the corresponding coefficients determined with the energy representation (ER) method. Since the MA enables us to finish the computation of the solvent reorganization term in less than 0.1 s once the coefficients are determined, the use of the MA enables us to provide an efficient computation of the HFE even for large, complex solutes. Through the applications, we find that our method has almost the same quantitative performance as the ER method with substantial reduction of the computational load.
Time accurate application of the MacCormack 2-4 scheme on massively parallel computers
NASA Technical Reports Server (NTRS)
Hudson, Dale A.; Long, Lyle N.
1995-01-01
Many recent computational efforts in turbulence and acoustics research have used higher order numerical algorithms. One popular method has been the explicit MacCormack 2-4 scheme. The MacCormack 2-4 scheme is second order accurate in time and fourth order accurate in space, and is stable for CFL's below 2/3. Current research has shown that the method can give accurate results but does exhibit significant Gibbs phenomena at sharp discontinuities. The impact of adding Jameson type second, third, and fourth order artificial viscosity was examined here. Category 2 problems, the nonlinear traveling wave and the Riemann problem, were computed using a CFL number of 0.25. This research has found that dispersion errors can be significantly reduced or nearly eliminated by using a combination of second and third order terms in the damping. Use of second and fourth order terms reduced the magnitude of dispersion errors but not as effectively as the second and third order combination. The program was coded using Thinking Machine's CM Fortran, a variant of Fortran 90/High Performance Fortran, and was executed on a 2K CM-200. Simple extrapolation boundary conditions were used for both problems.
New approach based on tetrahedral-mesh geometry for accurate 4D Monte Carlo patient-dose calculation
NASA Astrophysics Data System (ADS)
Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Kim, Seonghoon; Sohn, Jason W.
2015-02-01
In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using tetrahedral-mesh geometry based on the patient’s 4D CT data, (2) continuous movement/deformation of the tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the tetrahedral-mesh geometry and to directly transport radiation particles during continuous movement and deformation of the tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in tetrahedral-mesh geometry.
Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Kim, Seonghoon; Sohn, Jason W
2015-02-21
In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using tetrahedral-mesh geometry based on the patient's 4D CT data, (2) continuous movement/deformation of the tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the tetrahedral-mesh geometry and to directly transport radiation particles during continuous movement and deformation of the tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in tetrahedral-mesh geometry.
Erguel, Ozguer; Guerel, Levent
2008-12-01
We present a novel stabilization procedure for accurate surface formulations of electromagnetic scattering problems involving three-dimensional dielectric objects with arbitrarily low contrasts. Conventional surface integral equations provide inaccurate results for the scattered fields when the contrast of the object is low, i.e., when the electromagnetic material parameters of the scatterer and the host medium are close to each other. We propose a stabilization procedure involving the extraction of nonradiating currents and rearrangement of the right-hand side of the equations using fictitious incident fields. Then, only the radiating currents are solved to calculate the scattered fields accurately. This technique can easily be applied to the existing implementations of conventional formulations, it requires negligible extra computational cost, and it is also appropriate for the solution of large problems with the multilevel fast multipole algorithm. We show that the stabilization leads to robust formulations that are valid even for the solutions of extremely low-contrast objects.
Structural stability augmentation system design using BODEDIRECT: A quick and accurate approach
NASA Technical Reports Server (NTRS)
Goslin, T. J.; Ho, J. K.
1989-01-01
A methodology is presented for a modal suppression control law design using flight test data instead of mathematical models to obtain the required gain and phase information about the flexible airplane. This approach is referred to as BODEDIRECT. The purpose of the BODEDIRECT program is to provide a method of analyzing the modal phase relationships measured directly from the airplane. These measurements can be achieved with a frequency sweep at the control surface input while measuring the outputs of interest. The measured Bode-models can be used directly for analysis in the frequency domain, and for control law design. Besides providing a more accurate representation for the system inputs and outputs of interest, this method is quick and relatively inexpensive. To date, the BODEDIRECT program has been tested and verified for computational integrity. Its capabilities include calculation of series, parallel and loop closure connections between Bode-model representations. System PSD, together with gain and phase margins of stability may be calculated for successive loop closures of multi-input/multi-output systems. Current plans include extensive flight testing to obtain a Bode-model representation of a commercial aircraft for design of a structural stability augmentation system.
IDSite: An accurate approach to predict P450-mediated drug metabolism
Li, Jianing; Schneebeli, Severin T.; Bylund, Joseph; Farid, Ramy; Friesner, Richard A.
2011-01-01
Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets. PMID:22247702
Computer Algebra, Instrumentation and the Anthropological Approach
ERIC Educational Resources Information Center
Monaghan, John
2007-01-01
This article considers research and scholarship on the use of computer algebra in mathematics education following the instrumentation and the anthropological approaches. It outlines what these approaches are, positions them with regard to other approaches, examines tensions between the two approaches and makes suggestions for how work in this…
Computer-Based Training: An Institutional Approach.
ERIC Educational Resources Information Center
Barker, Philip; Manji, Karim
1992-01-01
Discussion of issues related to computer-assisted learning (CAL) and computer-based training (CBT) describes approaches to electronic learning; principles underlying courseware development to support these approaches; and a plan for creation of a CAL/CBT development center, including its functional role, campus services, staffing, and equipment…
Computational modelling approaches to vaccinology.
Pappalardo, Francesco; Flower, Darren; Russo, Giulia; Pennisi, Marzio; Motta, Santo
2015-02-01
Excepting the Peripheral and Central Nervous Systems, the Immune System is the most complex of somatic systems in higher animals. This complexity manifests itself at many levels from the molecular to that of the whole organism. Much insight into this confounding complexity can be gained through computational simulation. Such simulations range in application from epitope prediction through to the modelling of vaccination strategies. In this review, we evaluate selectively various key applications relevant to computational vaccinology: these include technique that operates at different scale that is, from molecular to organisms and even to population level.
Computational approaches to motor control.
Flash, T; Sejnowski, T J
2001-12-01
New concepts and computational models that integrate behavioral and neurophysiological observations have addressed several of the most fundamental long-standing problems in motor control. These problems include the selection of particular trajectories among the large number of possibilities, the solution of inverse kinematics and dynamics problems, motor adaptation and the learning of sequential behaviors.
Simple but accurate GCM-free approach for quantifying anthropogenic climate change
NASA Astrophysics Data System (ADS)
Lovejoy, S.
2014-12-01
We are so used to analysing the climate with the help of giant computer models (GCM's) that it is easy to get the impression that they are indispensable. Yet anthropogenic warming is so large (roughly 0.9oC) that it turns out that it is straightforward to quantify it with more empirically based methodologies that can be readily understood by the layperson. The key is to use the CO2 forcing as a linear surrogate for all the anthropogenic effects from 1880 to the present (implicitly including all effects due to Greenhouse Gases, aerosols and land use changes). To a good approximation, double the economic activity, double the effects. The relationship between the forcing and global mean temperature is extremely linear as can be seen graphically and understood without fancy statistics, [Lovejoy, 2014a] (see the attached figure and http://www.physics.mcgill.ca/~gang/Lovejoy.htm). To an excellent approximation, the deviations from the linear forcing - temperature relation can be interpreted as the natural variability. For example, this direct - yet accurate approach makes it graphically obvious that the "pause" or "hiatus" in the warming since 1998 is simply a natural cooling event that has roughly offset the anthropogenic warming [Lovejoy, 2014b]. Rather than trying to prove that the warming is anthropogenic, with a little extra work (and some nonlinear geophysics theory and pre-industrial multiproxies) we can disprove the competing theory that it is natural. This approach leads to the estimate that the probability of the industrial scale warming being a giant natural fluctuation is ≈0.1%: it can be dismissed. This destroys the last climate skeptic argument - that the models are wrong and the warming is natural. It finally allows for a closure of the debate. In this talk we argue that this new, direct, simple, intuitive approach provides an indispensable tool for communicating - and convincing - the public of both the reality and the amplitude of anthropogenic warming
Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao
2015-10-20
Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min.
Accurate and efficient computation of nonlocal potentials based on Gaussian-sum approximation
NASA Astrophysics Data System (ADS)
Exl, Lukas; Mauser, Norbert J.; Zhang, Yong
2016-12-01
We introduce an accurate and efficient method for the numerical evaluation of nonlocal potentials, including the 3D/2D Coulomb, 2D Poisson and 3D dipole-dipole potentials. Our method is based on a Gaussian-sum approximation of the singular convolution kernel combined with a Taylor expansion of the density. Starting from the convolution formulation of the nonlocal potential, for smooth and fast decaying densities, we make a full use of the Fourier pseudospectral (plane wave) approximation of the density and a separable Gaussian-sum approximation of the kernel in an interval where the singularity (the origin) is excluded. The potential is separated into a regular integral and a near-field singular correction integral. The first is computed with the Fourier pseudospectral method, while the latter is well resolved utilizing a low-order Taylor expansion of the density. Both parts are accelerated by fast Fourier transforms (FFT). The method is accurate (14-16 digits), efficient (O (Nlog N) complexity), low in storage, easily adaptable to other different kernels, applicable for anisotropic densities and highly parallelizable.
Li, Xiangrui; Lu, Zhong-Lin
2012-02-29
Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ (1) and DataPixx (2) use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher (3) described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network (4) and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements. Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect
A Museum Approach to Computer Learning.
ERIC Educational Resources Information Center
Wall, Roger
1986-01-01
Compares and contrasts the approaches taken by museums and schools in computer education. Reviews representative museum computer programs as "Keyboards for Kids" for preschool children of the Franklin Institute in Philadelphia and the teacher training project of Boston's Museum of Science. Offers perspectives on expanded program options.…
Application of the accurate mass and time tag approach in studies of the human blood lipidome
Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.
2008-01-01
We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. PMID:18502191
Time-Accurate Computation of Viscous Flow Around Deforming Bodies Using Overset Grids
Fast, P; Henshaw, W D
2001-04-02
Dynamically evolving boundaries and deforming bodies interacting with a flow are commonly encountered in fluid dynamics. However, the numerical simulation of flows with dynamic boundaries is difficult with current methods. We propose a new method for studying such problems. The key idea is to use the overset grid method with a thin, body-fitted grid near the deforming boundary, while using fixed Cartesian grids to cover most of the computational domain. Our approach combines the strengths of earlier moving overset grid methods for rigid body motion, and unstructured grid methods for Aow-structure interactions. Large scale deformation of the flow boundaries can be handled without a global regridding, and in a computationally efficient way. In terms of computational cost, even a full overset grid regridding is significantly cheaper than a full regridding of an unstructured grid for the same domain, especially in three dimensions. Numerical studies are used to verify accuracy and convergence of our flow solver. As a computational example, we consider two-dimensional incompressible flow past a flexible filament with prescribed dynamics.
Finding accurate frontiers: A knowledge-intensive approach to relational learning
NASA Technical Reports Server (NTRS)
Pazzani, Michael; Brunk, Clifford
1994-01-01
An approach to analytic learning is described that searches for accurate entailments of a Horn Clause domain theory. A hill-climbing search, guided by an information based evaluation function, is performed by applying a set of operators that derive frontiers from domain theories. The analytic learning system is one component of a multi-strategy relational learning system. We compare the accuracy of concepts learned with this analytic strategy to concepts learned with an analytic strategy that operationalizes the domain theory.
Enabling fast, stable and accurate peridynamic computations using multi-time-step integration
Lindsay, P.; Parks, M. L.; Prakash, A.
2016-04-13
Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, and computational cost is examined and several numerical examples are presented to corroborate the findings.
Enabling fast, stable and accurate peridynamic computations using multi-time-step integration
Lindsay, P.; Parks, M. L.; Prakash, A.
2016-04-13
Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less
When do perturbative approaches accurately capture the dynamics of complex quantum systems?
Fruchtman, Amir; Lambert, Neill; Gauger, Erik M.
2016-01-01
Understanding the dynamics of higher-dimensional quantum systems embedded in a complex environment remains a significant theoretical challenge. While several approaches yielding numerically converged solutions exist, these are computationally expensive and often provide only limited physical insight. Here we address the question: when do more intuitive and simpler-to-compute second-order perturbative approaches provide adequate accuracy? We develop a simple analytical criterion and verify its validity for the case of the much-studied FMO dynamics as well as the canonical spin-boson model. PMID:27335176
Toward exascale computing through neuromorphic approaches.
James, Conrad D.
2010-09-01
While individual neurons function at relatively low firing rates, naturally-occurring nervous systems not only surpass manmade systems in computing power, but accomplish this feat using relatively little energy. It is asserted that the next major breakthrough in computing power will be achieved through application of neuromorphic approaches that mimic the mechanisms by which neural systems integrate and store massive quantities of data for real-time decision making. The proposed LDRD provides a conceptual foundation for SNL to make unique advances toward exascale computing. First, a team consisting of experts from the HPC, MESA, cognitive and biological sciences and nanotechnology domains will be coordinated to conduct an exercise with the outcome being a concept for applying neuromorphic computing to achieve exascale computing. It is anticipated that this concept will involve innovative extension and integration of SNL capabilities in MicroFab, material sciences, high-performance computing, and modeling and simulation of neural processes/systems.
Accurate computation of surface stresses and forces with immersed boundary methods
NASA Astrophysics Data System (ADS)
Goza, Andres; Liska, Sebastian; Morley, Benjamin; Colonius, Tim
2016-09-01
Many immersed boundary methods solve for surface stresses that impose the velocity boundary conditions on an immersed body. These surface stresses may contain spurious oscillations that make them ill-suited for representing the physical surface stresses on the body. Moreover, these inaccurate stresses often lead to unphysical oscillations in the history of integrated surface forces such as the coefficient of lift. While the errors in the surface stresses and forces do not necessarily affect the convergence of the velocity field, it is desirable, especially in fluid-structure interaction problems, to obtain smooth and convergent stress distributions on the surface. To this end, we show that the equation for the surface stresses is an integral equation of the first kind whose ill-posedness is the source of spurious oscillations in the stresses. We also demonstrate that for sufficiently smooth delta functions, the oscillations may be filtered out to obtain physically accurate surface stresses. The filtering is applied as a post-processing procedure, so that the convergence of the velocity field is unaffected. We demonstrate the efficacy of the method by computing stresses and forces that converge to the physical stresses and forces for several test problems.
Toward accurate tooth segmentation from computed tomography images using a hybrid level set model
Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang E-mail: jing.xiong@siat.ac.cn; Hu, Ying; Xiong, Jing E-mail: jing.xiong@siat.ac.cn; Zhang, Jianwei
2015-01-15
Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0
Sahu, Nityananda; Gadre, Shridhar R
2015-01-07
In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm(-1) with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.
NASA Astrophysics Data System (ADS)
Sahu, Nityananda; Gadre, Shridhar R.
2015-01-01
In spite of the recent advents in parallel algorithms and computer hardware, high-level calculation of vibrational spectra of large molecules is still an uphill task. To overcome this, significant effort has been devoted to the development of new algorithms based on fragmentation methods. The present work provides the details of an efficient and accurate procedure for computing the vibrational spectra of large clusters employing molecular tailoring approach (MTA). The errors in the Hessian matrix elements and dipole derivatives arising due to the approximation nature of MTA are reduced by grafting the corrections from a smaller basis set. The algorithm has been tested out for obtaining vibrational spectra of neutral and charged water clusters at Møller-Plesset second order level of theory, and benchmarking them against the respective full calculation (FC) and/or experimental results. For (H2O)16 clusters, the estimated vibrational frequencies are found to differ by a maximum of 2 cm-1 with reference to the corresponding FC values. Unlike the FC, the MTA-based calculations including grafting procedure can be performed on a limited hardware, yet take a fraction of the FC time. The present methodology, thus, opens a possibility of the accurate estimation of the vibrational spectra of large molecular systems, which is otherwise impossible or formidable.
Bozkaya, Uğur
2013-10-21
The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials (IPs) from any level of theory, in principle. However, for non-variational methods, such as Møller-Plesset perturbation and coupled-cluster theories, the EKT computations can only be performed as by-products of analytic gradients as the relaxed generalized Fock matrix (GFM) and one- and two-particle density matrices (OPDM and TPDM, respectively) are required [J. Cioslowski, P. Piskorz, and G. Liu, J. Chem. Phys. 107, 6804 (1997)]. However, for the orbital-optimized methods both the GFM and OPDM are readily available and symmetric, as opposed to the standard post Hartree-Fock (HF) methods. Further, the orbital optimized methods solve the N-representability problem, which may arise when the relaxed particle density matrices are employed for the standard methods, by disregarding the orbital Z-vector contributions for the OPDM. Moreover, for challenging chemical systems, where spin or spatial symmetry-breaking problems are observed, the abnormal orbital response contributions arising from the numerical instabilities in the HF molecular orbital Hessian can be avoided by the orbital-optimization. Hence, it appears that the orbital-optimized methods are the most natural choice for the study of the EKT. In this research, the EKT for the orbital-optimized methods, such as orbital-optimized second- and third-order Møller-Plesset perturbation [U. Bozkaya, J. Chem. Phys. 135, 224103 (2011)] and coupled-electron pair theories [OCEPA(0)] [U. Bozkaya and C. D. Sherrill, J. Chem. Phys. 139, 054104 (2013)], are presented. The presented methods are applied to IPs of the second- and third-row atoms, and closed- and open-shell molecules. Performances of the orbital-optimized methods are compared with those of the counterpart standard methods. Especially, results of the OCEPA(0) method (with the aug-cc-pVTZ basis set) for the lowest IPs of the considered atoms and closed
Accurate electronic-structure description of Mn complexes: a GGA+U approach
NASA Astrophysics Data System (ADS)
Li, Elise Y.; Kulik, Heather; Marzari, Nicola
2008-03-01
Conventional density-functional approach often fail in offering an accurate description of the spin-resolved energetics in transition metals complexes. We will focus here on Mn complexes, where many aspects of the molecular structure and the reaction mechanisms are still unresolved - most notably in the oxygen-evolving complex (OEC) of photosystem II and the manganese catalase (MC). We apply a self-consistent GGA + U approach [1], originally designed within the DFT framework for the treatment of strongly correlated materials, to describe the geometry, the electronic and the magnetic properties of various manganese oxide complexes, finding very good agreement with higher-order ab-initio calculations. In particular, the different oxidation states of dinuclear systems containing the [Mn2O2]^n+ (n= 2, 3, 4) core are investigated, in order to mimic the basic face unit of the OEC complex. [1]. H. J. Kulik, M. Cococcioni, D. A. Scherlis, N. Marzari, Phys. Rev. Lett., 2006, 97, 103001
A Creative Arts Approach to Computer Programming.
ERIC Educational Resources Information Center
Greenberg, Gary
1991-01-01
Discusses "Object LOGO," a symbolic computer programing language for use in the creative arts. Describes the use of the program in approaching arts projects from textual, graphic, and musical perspectives. Suggests that use of the program can promote development of creative skills and humanities learning in general. (SG)
Accurate potential energy surfaces with a DFT+U(R) approach.
Kulik, Heather J; Marzari, Nicola
2011-11-21
We introduce an improvement to the Hubbard U augmented density functional approach known as DFT+U that incorporates variations in the value of self-consistently calculated, linear-response U with changes in geometry. This approach overcomes the one major shortcoming of previous DFT+U studies, i.e., the use of an averaged Hubbard U when comparing energies for different points along a potential energy surface is no longer required. While DFT+U is quite successful at providing accurate descriptions of localized electrons (e.g., d or f) by correcting self-interaction errors of standard exchange correlation functionals, we show several diatomic molecule examples where this position-dependent DFT+U(R) provides a significant two- to four-fold improvement over DFT+U predictions, when compared to accurate correlated quantum chemistry and experimental references. DFT+U(R) reduces errors in binding energies, frequencies, and equilibrium bond lengths by applying the linear-response, position-dependent U(R) at each configuration considered. This extension is most relevant where variations in U are large across the points being compared, as is the case with covalent diatomic molecules such as transition-metal oxides. We thus provide a tool for deciding whether a standard DFT+U approach is sufficient by determining the strength of the dependence of U on changes in coordinates. We also apply this approach to larger systems with greater degrees of freedom and demonstrate how DFT+U(R) may be applied automatically in relaxations, transition-state finding methods, and dynamics.
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach.
Opgen-Rhein, Rainer; Strimmer, Korbinian
2007-01-01
High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc modifications of the ordinary t statistic to complicated hierarchical Bayesian models. Here, we introduce the "shrinkage t" statistic that is based on a novel and model-free shrinkage estimate of the variance vector across genes. This is derived in a quasi-empirical Bayes setting. The new rank score is fully automatic and requires no specification of parameters or distributions. It is computationally inexpensive and can be written analytically in closed form. Using a series of synthetic and three real expression data we studied the quality of gene rankings produced by the "shrinkage t" statistic. The new score consistently leads to highly accurate rankings for the complete range of investigated data sets and all considered scenarios for across-gene variance structures.
Balzar, D.; Ledbetter, H.
1995-12-31
In the {open_quotes}double-Voigt{close_quotes} approach, an exact Voigt function describes both size- and strain-broadened profiles. The lattice strain is defined in terms of physically credible mean-square strain averaged over a distance in the diffracting domains. Analysis of Fourier coefficients in a harmonic approximation for strain coefficients leads to the Warren-Averbach method for the separation of size and strain contributions to diffraction line broadening. The model is introduced in the Rietveld refinement program in the following way: Line widths are modeled with only four parameters in the isotropic case. Varied parameters are both surface- and volume-weighted domain sizes and root-mean-square strains averaged over two distances. Refined parameters determine the physically broadened Voigt line profile. Instrumental Voigt line profile parameters are added to obtain the observed (Voigt) line profile. To speed computation, the corresponding pseudo-Voigt function is calculated and used as a fitting function in refinement. This approach allows for both fast computer code and accurate modeling in terms of physically identifiable parameters.
NASA Technical Reports Server (NTRS)
Emmons, Louisa; De Zafra, Robert
1991-01-01
A simple method for milling accurate off-axis parabolic mirrors with a computer-controlled milling machine is discussed. For machines with a built-in circle-cutting routine, an exact paraboloid can be milled with few computer commands and without the use of the spherical or linear approximations. The proposed method can be adapted easily to cut off-axis sections of elliptical or spherical mirrors.
Computational Approach for Developing Blood Pump
NASA Technical Reports Server (NTRS)
Kwak, Dochan
2002-01-01
This viewgraph presentation provides an overview of the computational approach to developing a ventricular assist device (VAD) which utilizes NASA aerospace technology. The VAD is used as a temporary support to sick ventricles for those who suffer from late stage congestive heart failure (CHF). The need for donor hearts is much greater than their availability, and the VAD is seen as a bridge-to-transplant. The computational issues confronting the design of a more advanced, reliable VAD include the modelling of viscous incompressible flow. A computational approach provides the possibility of quantifying the flow characteristics, which is especially valuable for analyzing compact design with highly sensitive operating conditions. Computational fluid dynamics (CFD) and rocket engine technology has been applied to modify the design of a VAD which enabled human transplantation. The computing requirement for this project is still large, however, and the unsteady analysis of the entire system from natural heart to aorta involves several hundred revolutions of the impeller. Further study is needed to assess the impact of mechanical VADs on the human body
NASA Astrophysics Data System (ADS)
Garrison, Stephen L.
2005-07-01
The combination of molecular simulations and potentials obtained from quantum chemistry is shown to be able to provide reasonably accurate thermodynamic property predictions. Gibbs ensemble Monte Carlo simulations are used to understand the effects of small perturbations to various regions of the model Lennard-Jones 12-6 potential. However, when the phase behavior and second virial coefficient are scaled by the critical properties calculated for each potential, the results obey a corresponding states relation suggesting a non-uniqueness problem for interaction potentials fit to experimental phase behavior. Several variations of a procedure collectively referred to as quantum mechanical Hybrid Methods for Interaction Energies (HM-IE) are developed and used to accurately estimate interaction energies from CCSD(T) calculations with a large basis set in a computationally efficient manner for the neon-neon, acetylene-acetylene, and nitrogen-benzene systems. Using these results and methods, an ab initio, pairwise-additive, site-site potential for acetylene is determined and then improved using results from molecular simulations using this initial potential. The initial simulation results also indicate that a limited range of energies important for accurate phase behavior predictions. Second virial coefficients calculated from the improved potential indicate that one set of experimental data in the literature is likely erroneous. This prescription is then applied to methanethiol. Difficulties in modeling the effects of the lone pair electrons suggest that charges on the lone pair sites negatively impact the ability of the intermolecular potential to describe certain orientations, but that the lone pair sites may be necessary to reasonably duplicate the interaction energies for several orientations. Two possible methods for incorporating the effects of three-body interactions into simulations within the pairwise-additivity formulation are also developed. A low density
NASA Astrophysics Data System (ADS)
Annecchione, Maria; Hatch, David; Hefford, Shane W.
2017-01-01
In this paper we investigate digital elevation model (DEM) sourcing requirements to compute gravity gradiometry terrain corrections accurate to 1 Eötvös (Eö) at observation heights of 80 m or more above ground. Such survey heights are typical in fixed-wing airborne surveying for resource exploration where the maximum signal-to-noise ratio is sought. We consider the accuracy of terrain corrections relevant for recent commercial airborne gravity gradiometry systems operating at the 10 Eö noise level and for future systems with a target noise level of 1 Eö. We focus on the requirements for the vertical gradient of the vertical component of gravity (Gdd) because this element of the gradient tensor is most commonly interpreted qualitatively and quantitatively. Terrain correction accuracy depends on the bare-earth DEM accuracy and spatial resolution. The bare-earth DEM accuracy and spatial resolution depends on its source. Two possible sources are considered: airborne LiDAR and Shuttle Radar Topography Mission (SRTM). The accuracy of an SRTM DEM is affected by vegetation height. The SRTM footprint is also larger and the DEM resolution is thus lower. However, resolution requirements relax as relief decreases. Publicly available LiDAR data and 1 arc-second and 3 arc-second SRTM data were selected over four study areas representing end member cases of vegetation cover and relief. The four study areas are presented as reference material for processing airborne gravity gradiometry data at the 1 Eö noise level with 50 m spatial resolution. From this investigation we find that to achieve 1 Eö accuracy in the terrain correction at 80 m height airborne LiDAR data are required even when terrain relief is a few tens of meters and the vegetation is sparse. However, as satellite ranging technologies progress bare-earth DEMs of sufficient accuracy and resolution may be sourced at lesser cost. We found that a bare-earth DEM of 10 m resolution and 2 m accuracy are sufficient for
Computational approach for probing the flow through artificial heart devices.
Kiris, C; Kwak, D; Rogers, S; Chang, I D
1997-11-01
Computational fluid dynamics (CFD) has become an indispensable part of aerospace research and design. The solution procedure for incompressible Navier-Stokes equations can be used for biofluid mechanics research. The computational approach provides detailed knowledge of the flowfield complementary to that obtained by experimental measurements. This paper illustrates the extension of CFD techniques to artificial heart flow simulation. Unsteady incompressible Navier-Stokes equations written in three-dimensional generalized curvilinear coordinates are solved iteratively at each physical time step until the incompressibility condition is satisfied. The solution method is based on the pseudocompressibility approach. It uses an implicit upwind-differencing scheme together with the Gauss-Seidel line-relaxation method. The efficiency and robustness of the time-accurate formulation of the numerical algorithm are tested by computing the flow through model geometries. A channel flow with a moving indentation is computed and validated by experimental measurements and other numerical solutions. In order to handle the geometric complexity and the moving boundary problems, a zonal method and an overlapped grid embedding scheme are employed, respectively. Steady-state solutions for the flow through a tilting-disk heart valve are compared with experimental measurements. Good agreement is obtained. Aided by experimental data, the flow through an entire Penn State artificial heart model is computed.
Ustinov, E. A.
2014-10-07
Commensurate–incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs–Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton–graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton–carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas–solid and solid–solid system.
Ustinov, E A
2014-10-07
Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system.
A Maximum-Entropy approach for accurate document annotation in the biomedical domain
2012-01-01
The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the search and the quality of the results. Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information and makes one step further towards the Semantic Web. A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task. In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with terms from the Medical Subject Headings (MeSH). The experimental evaluation shows that the suggested Maximum Entropy approach for annotating biomedical documents with MeSH terms is highly accurate, robust to the ambiguity of terms, and can provide very good performance even when a very small number of training documents is used. More precisely, we show that the proposed algorithm obtained an average F-measure of 92.4% (precision 99.41%, recall 86.77%) for the full range of the explored terms (4,078 MeSH terms), and that the algorithm’s performance is resilient to terms’ ambiguity, achieving an average F-measure of 92.42% (precision 99.32%, recall 86.87%) in the explored MeSH terms which were found to be ambiguous according to the Unified Medical Language System (UMLS) thesaurus. Finally, we compared the results of the suggested methodology with a Naive Bayes and a Decision Trees classification approach, and we show that the Maximum Entropy based approach performed with higher F-Measure in both ambiguous and monosemous MeSH terms. PMID:22541593
A Maximum-Entropy approach for accurate document annotation in the biomedical domain.
Tsatsaronis, George; Macari, Natalia; Torge, Sunna; Dietze, Heiko; Schroeder, Michael
2012-04-24
The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the search and the quality of the results. Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information and makes one step further towards the Semantic Web. A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task. In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with terms from the Medical Subject Headings (MeSH).The experimental evaluation shows that the suggested Maximum Entropy approach for annotating biomedical documents with MeSH terms is highly accurate, robust to the ambiguity of terms, and can provide very good performance even when a very small number of training documents is used. More precisely, we show that the proposed algorithm obtained an average F-measure of 92.4% (precision 99.41%, recall 86.77%) for the full range of the explored terms (4,078 MeSH terms), and that the algorithm's performance is resilient to terms' ambiguity, achieving an average F-measure of 92.42% (precision 99.32%, recall 86.87%) in the explored MeSH terms which were found to be ambiguous according to the Unified Medical Language System (UMLS) thesaurus. Finally, we compared the results of the suggested methodology with a Naive Bayes and a Decision Trees classification approach, and we show that the Maximum Entropy based approach performed with higher F-Measure in both ambiguous and monosemous MeSH terms.
NASA Astrophysics Data System (ADS)
Römer, Ulrich; Schöps, Sebastian; De Gersem, Herbert
2017-04-01
In electromagnetic simulations of magnets and machines, one is often interested in a highly accurate and local evaluation of the magnetic field uniformity. Based on local post-processing of the solution, a defect correction scheme is proposed as an easy to realize alternative to higher order finite element or hybrid approaches. Radial basis functions (RBFs) are key for the generality of the method, which in particular can handle unstructured grids. Also, contrary to conventional finite element basis functions, higher derivatives of the solution can be evaluated, as required, e.g., for deflection magnets. Defect correction is applied to obtain a solution with improved accuracy and adjoint techniques are used to estimate the remaining error for a specific quantity of interest. Significantly improved (local) convergence orders are obtained. The scheme is also applied to the simulation of a Stern-Gerlach magnet currently in operation.
Computational Approaches to Nucleic Acid Origami.
Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo
2015-10-12
Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.
Computational approach to compact Riemann surfaces
NASA Astrophysics Data System (ADS)
Frauendiener, Jörg; Klein, Christian
2017-01-01
A purely numerical approach to compact Riemann surfaces starting from plane algebraic curves is presented. The critical points of the algebraic curve are computed via a two-dimensional Newton iteration. The starting values for this iteration are obtained from the resultants with respect to both coordinates of the algebraic curve and a suitable pairing of their zeros. A set of generators of the fundamental group for the complement of these critical points in the complex plane is constructed from circles around these points and connecting lines obtained from a minimal spanning tree. The monodromies are computed by solving the defining equation of the algebraic curve on collocation points along these contours and by analytically continuing the roots. The collocation points are chosen to correspond to Chebychev collocation points for an ensuing Clenshaw-Curtis integration of the holomorphic differentials which gives the periods of the Riemann surface with spectral accuracy. At the singularities of the algebraic curve, Puiseux expansions computed by contour integration on the circles around the singularities are used to identify the holomorphic differentials. The Abel map is also computed with the Clenshaw-Curtis algorithm and contour integrals. As an application of the code, solutions to the Kadomtsev-Petviashvili equation are computed on non-hyperelliptic Riemann surfaces.
A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus
Li, Ruichao; Chiou, Jiachi; Chan, Edward Wai-Chi; Chen, Sheng
2016-01-01
A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the blaCARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that blaCARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this blaCARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of blaCARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by blaCARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification. PMID:26858713
Esque, Jeremy; Cecchini, Marco
2015-04-23
The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.
Digital test signal generation: An accurate SNR calibration approach for the DSN
NASA Technical Reports Server (NTRS)
Gutierrez-Luaces, Benito O.
1993-01-01
In support of the on-going automation of the Deep Space Network (DSN) a new method of generating analog test signals with accurate signal-to-noise ratio (SNR) is described. High accuracy is obtained by simultaneous generation of digital noise and signal spectra at the desired bandwidth (base-band or bandpass). The digital synthesis provides a test signal embedded in noise with the statistical properties of a stationary random process. Accuracy is dependent on test integration time and limited only by the system quantization noise (0.02 dB). The monitor and control as well as signal-processing programs reside in a personal computer (PC). Commands are transmitted to properly configure the specially designed high-speed digital hardware. The prototype can generate either two data channels modulated or not on a subcarrier, or one QPSK channel, or a residual carrier with one biphase data channel. The analog spectrum generated is on the DC to 10 MHz frequency range. These spectra may be up-converted to any desired frequency without loss on the characteristics of the SNR provided. Test results are presented.
Launay, David; Sobanski, Vincent; Dussart, Patricia; Chafey, Philippe; Broussard, Cédric; Duban-Deweer, Sophie; Vermersch, Patrick; Prin, Lionel; Lefranc, Didier
2015-01-01
Serological proteome analysis (SERPA) combines classical proteomic technology with effective separation of cellular protein extracts on two-dimensional gel electrophoresis, western blotting, and identification of the antigenic spot of interest by mass spectrometry. A critical point is related to the antigenic target characterization by mass spectrometry, which depends on the accuracy of the matching of antigenic reactivities on the protein spots during the 2D immunoproteomic procedures. The superimposition, based essentially on visual criteria of antigenic and protein spots, remains the major limitation of SERPA. The introduction of fluorescent dyes in proteomic strategies, commonly known as 2D-DIGE (differential in-gel electrophoresis), has boosted the qualitative capabilities of 2D electrophoresis. Based on this 2D-DIGE strategy, we have improved the conventional SERPA by developing a new and entirely fluorescence-based bi-dimensional immunoproteomic (FBIP) analysis, performed with three fluorescent dyes. To optimize the alignment of the different antigenic maps, we introduced a landmark map composed of a combination of specific antibodies. This methodological development allows simultaneous revelation of the antigenic, landmark and proteomic maps on each immunoblot. A computer-assisted process using commercially available software automatically leads to the superimposition of the different maps, ensuring accurate localization of antigenic spots of interest. PMID:26132557
Sun, Y Y; Kim, Yong-Hyun; Lee, Kyuho; Zhang, S B
2008-10-21
Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.
Computer Forensics Education - the Open Source Approach
NASA Astrophysics Data System (ADS)
Huebner, Ewa; Bem, Derek; Cheung, Hon
In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.
Computational Approaches for Predicting Biomedical Research Collaborations
Zhang, Qing; Yu, Hong
2014-01-01
Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets. PMID:25375164
Computational approaches to fMRI analysis.
Cohen, Jonathan D; Daw, Nathaniel; Engelhardt, Barbara; Hasson, Uri; Li, Kai; Niv, Yael; Norman, Kenneth A; Pillow, Jonathan; Ramadge, Peter J; Turk-Browne, Nicholas B; Willke, Theodore L
2017-02-23
Analysis methods in cognitive neuroscience have not always matched the richness of fMRI data. Early methods focused on estimating neural activity within individual voxels or regions, averaged over trials or blocks and modeled separately in each participant. This approach mostly neglected the distributed nature of neural representations over voxels, the continuous dynamics of neural activity during tasks, the statistical benefits of performing joint inference over multiple participants and the value of using predictive models to constrain analysis. Several recent exploratory and theory-driven methods have begun to pursue these opportunities. These methods highlight the importance of computational techniques in fMRI analysis, especially machine learning, algorithmic optimization and parallel computing. Adoption of these techniques is enabling a new generation of experiments and analyses that could transform our understanding of some of the most complex-and distinctly human-signals in the brain: acts of cognition such as thoughts, intentions and memories.
Computational Approach to Hyperelliptic Riemann Surfaces
NASA Astrophysics Data System (ADS)
Frauendiener, Jörg; Klein, Christian
2015-03-01
We present a computational approach to general hyperelliptic Riemann surfaces in Weierstrass normal form. The surface is given by a list of the branch points, the coefficients of the defining polynomial or a system of cuts for the curve. A canonical basis of the homology is introduced algorithmically for this curve. The periods of the holomorphic differentials and the Abel map are computed with the Clenshaw-Curtis method to achieve spectral accuracy. The code can handle almost degenerate Riemann surfaces. This work generalizes previous work on real hyperelliptic surfaces with prescribed cuts to arbitrary hyperelliptic surfaces. As an example, solutions to the sine-Gordon equation in terms of multi-dimensional theta functions are studied, also in the solitonic limit of these solutions.
A fourth order accurate finite difference scheme for the computation of elastic waves
NASA Technical Reports Server (NTRS)
Bayliss, A.; Jordan, K. E.; Lemesurier, B. J.; Turkel, E.
1986-01-01
A finite difference for elastic waves is introduced. The model is based on the first order system of equations for the velocities and stresses. The differencing is fourth order accurate on the spatial derivatives and second order accurate in time. The model is tested on a series of examples including the Lamb problem, scattering from plane interf aces and scattering from a fluid-elastic interface. The scheme is shown to be effective for these problems. The accuracy and stability is insensitive to the Poisson ratio. For the class of problems considered here it is found that the fourth order scheme requires for two-thirds to one-half the resolution of a typical second order scheme to give comparable accuracy.
A computational language approach to modeling prose recall in schizophrenia.
Rosenstein, Mark; Diaz-Asper, Catherine; Foltz, Peter W; Elvevåg, Brita
2014-06-01
Many cortical disorders are associated with memory problems. In schizophrenia, verbal memory deficits are a hallmark feature. However, the exact nature of this deficit remains elusive. Modeling aspects of language features used in memory recall have the potential to provide means for measuring these verbal processes. We employ computational language approaches to assess time-varying semantic and sequential properties of prose recall at various retrieval intervals (immediate, 30 min and 24 h later) in patients with schizophrenia, unaffected siblings and healthy unrelated control participants. First, we model the recall data to quantify the degradation of performance with increasing retrieval interval and the effect of diagnosis (i.e., group membership) on performance. Next we model the human scoring of recall performance using an n-gram language sequence technique, and then with a semantic feature based on Latent Semantic Analysis. These models show that automated analyses of the recalls can produce scores that accurately mimic human scoring. The final analysis addresses the validity of this approach by ascertaining the ability to predict group membership from models built on the two classes of language features. Taken individually, the semantic feature is most predictive, while a model combining the features improves accuracy of group membership prediction slightly above the semantic feature alone as well as over the human rating approach. We discuss the implications for cognitive neuroscience of such a computational approach in exploring the mechanisms of prose recall.
NASA Technical Reports Server (NTRS)
Goodwin, Sabine A.; Raj, P.
1999-01-01
Progress to date towards the development and validation of a fast, accurate and cost-effective aeroelastic method for advanced parallel computing platforms such as the IBM SP2 and the SGI Origin 2000 is presented in this paper. The ENSAERO code, developed at the NASA-Ames Research Center has been selected for this effort. The code allows for the computation of aeroelastic responses by simultaneously integrating the Euler or Navier-Stokes equations and the modal structural equations of motion. To assess the computational performance and accuracy of the ENSAERO code, this paper reports the results of the Navier-Stokes simulations of the transonic flow over a flexible aeroelastic wing body configuration. In addition, a forced harmonic oscillation analysis in the frequency domain and an analysis in the time domain are done on a wing undergoing a rigid pitch and plunge motion. Finally, to demonstrate the ENSAERO flutter-analysis capability, aeroelastic Euler and Navier-Stokes computations on an L-1011 wind tunnel model including pylon, nacelle and empennage are underway. All computational solutions are compared with experimental data to assess the level of accuracy of ENSAERO. As the computations described above are performed, a meticulous log of computational performance in terms of wall clock time, execution speed, memory and disk storage is kept. Code scalability is also demonstrated by studying the impact of varying the number of processors on computational performance on the IBM SP2 and the Origin 2000 systems.
FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins.
Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A
2008-09-04
A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford-Schellman integral if the proteins contain more than approximately 20-25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pK a's of the ionizable groups of these proteins within an average absolute value of 0.4 p K units and a maximum error of 1.2 p K units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford-Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and
Sculpting the band gap: a computational approach
Prasai, Kiran; Biswas, Parthapratim; Drabold, D. A.
2015-01-01
Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations. PMID:26490203
Sculpting the band gap: a computational approach
NASA Astrophysics Data System (ADS)
Prasai, Kiran; Biswas, Parthapratim; Drabold, D. A.
2015-10-01
Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations.
NASA Astrophysics Data System (ADS)
Huré, J.-M.; Hersant, F.
2017-02-01
We compute the structure of a self-gravitating torus with polytropic equation of state (EOS) rotating in an imposed centrifugal potential. The Poisson solver is based on isotropic multigrid with optimal covering factor (fluid section-to-grid area ratio). We work at second order in the grid resolution for both finite difference and quadrature schemes. For soft EOS (i.e. polytropic index n ≥ 1), the underlying second order is naturally recovered for boundary values and any other integrated quantity sensitive to the mass density (mass, angular momentum, volume, virial parameter, etc.), i.e. errors vary with the number N of nodes per direction as ˜1/N2. This is, however, not observed for purely geometrical quantities (surface area, meridional section area, volume), unless a subgrid approach is considered (i.e. boundary detection). Equilibrium sequences are also much better described, especially close to critical rotation. Yet another technical effort is required for hard EOS (n < 1), due to infinite mass density gradients at the fluid surface. We fix the problem by using kernel splitting. Finally, we propose an accelerated version of the self-consistent field (SCF) algorithm based on a node-by-node pre-conditioning of the mass density at each step. The computing time is reduced by a factor of 2 typically, regardless of the polytropic index. There is a priori no obstacle to applying these results and techniques to ellipsoidal configurations and even to 3D configurations.
NASA Astrophysics Data System (ADS)
Ng, C. N.; Chu, T. P.; Wu, Huasheng; Tong, S. Y.; Huang, Hong
1997-03-01
We compare multiple scattering results of angle-resolved photoelectron diffraction spectra between the exact slab method and the separable propagator perturbation method. In the slab method,footnote C.H. Li, A.R. Lubinsky and S.Y. Tong, Phys. Rev. B17, 3128 (1978). the source wave and multiple scattering within the strong scattering atomic layers are expanded in spherical waves while interlayer scattering is expressed in plane waves. The transformation between spherical waves and plane waves is done exactly. The plane waves are then matched across the solid-vacuum interface to a single outgoing plane wave in the detector's direction. The separable propagator perturbation approach uses two approximations: (i) A separable representation of the Green's function propagator and (ii) A perturbation expansion of multiple scattering terms. Results of c(2x2) S-Ni(001) show that this approximate method fails to converge due to the very slow convergence of the separable representation for scattering angles less than 90^circ. However, this method is accurate in the backscattering regime and may be applied to XAFS calculations.(J.J. Rehr and R.C. Albers, Phys. Rev. B41, 8139 (1990).) The use of this method for angle-resolved photoelectron diffraction spectra is substantially less reliable.
Bonetto, Paola; Qi, Jinyi; Leahy, Richard M.
1999-10-01
We describe a method for computing linear observer statistics for maximum a posteriori (MAP) reconstructions of PET images. The method is based on a theoretical approximation for the mean and covariance of MAP reconstructions. In particular, we derive here a closed form for the channelized Hotelling observer (CHO) statistic applied to 2D MAP images. We show reasonably good correspondence between these theoretical results and Monte Carlo studies. The accuracy and low computational cost of the approximation allow us to analyze the observer performance over a wide range of operating conditions and parameter settings for the MAP reconstruction algorithm.
Time-Accurate Computations of Isolated Circular Synthetic Jets in Crossflow
NASA Technical Reports Server (NTRS)
Rumsey, C. L.; Schaeffler, N. W.; Milanovic, I. M.; Zaman, K. B. M. Q.
2007-01-01
Results from unsteady Reynolds-averaged Navier-Stokes computations are described for two different synthetic jet flows issuing into a turbulent boundary layer crossflow through a circular orifice. In one case the jet effect is mostly contained within the boundary layer, while in the other case the jet effect extends beyond the boundary layer edge. Both cases have momentum flux ratios less than 2. Several numerical parameters are investigated, and some lessons learned regarding the CFD methods for computing these types of flow fields are summarized. Results in both cases are compared to experiment.
Computational approaches to motor learning by imitation.
Schaal, Stefan; Ijspeert, Auke; Billard, Aude
2003-01-01
Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking-indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions. PMID:12689379
ERIC Educational Resources Information Center
Steiger, James H.
1979-01-01
The program presented computes a chi-square statistic for testing pattern hypotheses on correlation matrices. The statistic is based on a multivariate generalization of the Fisher r-to-z transformation. This statistic has small sample performance which is superior to an analogous likelihood ratio statistic obtained via the analysis of covariance…
Krokhotin, Andrey; Dokholyan, Nikolay V
2015-01-01
Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.
Computational approaches for RNA energy parameter estimation
Andronescu, Mirela; Condon, Anne; Hoos, Holger H.; Mathews, David H.; Murphy, Kevin P.
2010-01-01
Methods for efficient and accurate prediction of RNA structure are increasingly valuable, given the current rapid advances in understanding the diverse functions of RNA molecules in the cell. To enhance the accuracy of secondary structure predictions, we developed and refined optimization techniques for the estimation of energy parameters. We build on two previous approaches to RNA free-energy parameter estimation: (1) the Constraint Generation (CG) method, which iteratively generates constraints that enforce known structures to have energies lower than other structures for the same molecule; and (2) the Boltzmann Likelihood (BL) method, which infers a set of RNA free-energy parameters that maximize the conditional likelihood of a set of reference RNA structures. Here, we extend these approaches in two main ways: We propose (1) a max-margin extension of CG, and (2) a novel linear Gaussian Bayesian network that models feature relationships, which effectively makes use of sparse data by sharing statistical strength between parameters. We obtain significant improvements in the accuracy of RNA minimum free-energy pseudoknot-free secondary structure prediction when measured on a comprehensive set of 2518 RNA molecules with reference structures. Our parameters can be used in conjunction with software that predicts RNA secondary structures, RNA hybridization, or ensembles of structures. Our data, software, results, and parameter sets in various formats are freely available at http://www.cs.ubc.ca/labs/beta/Projects/RNA-Params. PMID:20940338
Solubility of nonelectrolytes: a first-principles computational approach.
Jackson, Nicholas E; Chen, Lin X; Ratner, Mark A
2014-05-15
Using a combination of classical molecular dynamics and symmetry adapted intermolecular perturbation theory, we develop a high-accuracy computational method for examining the solubility energetics of nonelectrolytes. This approach is used to accurately compute the cohesive energy density and Hildebrand solubility parameters of 26 molecular liquids. The energy decomposition of symmetry adapted perturbation theory is then utilized to develop multicomponent Hansen-like solubility parameters. These parameters are shown to reproduce the solvent categorizations (nonpolar, polar aprotic, or polar protic) of all molecular liquids studied while lending quantitative rigor to these qualitative categorizations via the introduction of simple, easily computable parameters. Notably, we find that by monitoring the first-order exchange energy contribution to the total interaction energy, one can rigorously determine the hydrogen bonding character of a molecular liquid. Finally, this method is applied to compute explicitly the Flory interaction parameter and the free energy of mixing for two different small molecule mixtures, reproducing the known miscibilities. This methodology represents an important step toward the prediction of molecular solubility from first principles.
Matrix-vector multiplication using digital partitioning for more accurate optical computing
NASA Technical Reports Server (NTRS)
Gary, C. K.
1992-01-01
Digital partitioning offers a flexible means of increasing the accuracy of an optical matrix-vector processor. This algorithm can be implemented with the same architecture required for a purely analog processor, which gives optical matrix-vector processors the ability to perform high-accuracy calculations at speeds comparable with or greater than electronic computers as well as the ability to perform analog operations at a much greater speed. Digital partitioning is compared with digital multiplication by analog convolution, residue number systems, and redundant number representation in terms of the size and the speed required for an equivalent throughput as well as in terms of the hardware requirements. Digital partitioning and digital multiplication by analog convolution are found to be the most efficient alogrithms if coding time and hardware are considered, and the architecture for digital partitioning permits the use of analog computations to provide the greatest throughput for a single processor.
2014-10-08
Marenich, Christopher J. Cramer, Donald G. Truhlar, and Chang-Guo Zhan. Free Energies of Solvation with Surface , Volume, and Local Electrostatic...Effects and Atomic Surface Tensions to Represent the First Solvation Shell (Reprint), Journal of Chemical Theory and Computation, (01 2010): . doi...the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models, Physical Chemistry
An Accurate Method to Compute the Parasitic Electromagnetic Radiations of Real Solar Panels
NASA Astrophysics Data System (ADS)
Andreiu, G.; Panh, J.; Reineix, A.; Pelissou, P.; Girard, C.; Delannoy, P.; Romeuf, X.; Schmitt, D.
2012-05-01
The methodology [1] able to compute the parasitic electromagnetic (EM) radiations of a solar panel is highly improved in this paper to model real solar panels. Thus, honeycomb composite panels, triple junction solar cells and serie or shunt regulation system can now be taken into account. After a brief summary of the methodology, the improvements are detailed. Finally, some encouraging frequency and time-domain results of magnetic field emitted by a real solar panel are presented.
NASA Technical Reports Server (NTRS)
Ellison, Donald; Conway, Bruce; Englander, Jacob
2015-01-01
A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.
Accurate computation of weights in classical Gauss-Christoffel quadrature rules
Yakimiw, E.
1996-12-01
For many classical Gauss-Christoffel quadrature rules there does not exist a method which guarantees a uniform level of accuracy for the Gaussian quadrature weights at all quadrature nodes unless the nodes are known exactly. More disturbing, some algebraic expressions for these weights exhibit an excessive sensitivity to even the smallest perturbations in the node location. This sensitivity rapidly increases with high order quadrature rules. Current uses of very high order quadratures are common with the advent of more powerful computers, and a loss of accuracy in the weights has become a problem and must be addressed. A simple but efficient and general method for improving the accuracy of the computation of the quadrature weights even though the nodes may carry a significant large error. In addition, a highly efficient root-finding iterative technique with superlinear converging rates for computing the nodes is developed. It uses solely the quadrature polynomials and their first derivatives. A comparison of this method with the eigenvalue method of Golub and Welsh implemented in most standard software libraries is made. The proposed method outperforms the latter from the point of view of both accuracy and efficiency. The Legendre, Lobatto, Radau, Hermite, and Laguerre quadrature rules are examined. 22 refs., 7 figs., 5 tabs.
NASA Technical Reports Server (NTRS)
Vaughan, William W.; Friedman, Mark J.; Monteiro, Anand C.
1993-01-01
In earlier papers, Doedel and the authors have developed a numerical method and derived error estimates for the computation of branches of heteroclinic orbits for a system of autonomous ordinary differential equations in R(exp n). The idea of the method is to reduce a boundary value problem on the real line to a boundary value problem on a finite interval by using a local (linear or higher order) approximation of the stable and unstable manifolds. A practical limitation for the computation of homoclinic and heteroclinic orbits has been the difficulty in obtaining starting orbits. Typically these were obtained from a closed form solution or via a homotopy from a known solution. Here we consider extensions of our algorithm which allow us to obtain starting orbits on the continuation branch in a more systematic way as well as make the continuation algorithm more flexible. In applications, we use the continuation software package AUTO in combination with some initial value software. The examples considered include computation of homoclinic orbits in a singular perturbation problem and in a turbulent fluid boundary layer in the wall region problem.
Johnson, K.A.; Holman, B.L.; Rosen, T.J.; Nagel, J.S.; English, R.J.; Growdon, J.H. )
1990-04-01
To determine the diagnostic accuracy of iofetamine hydrochloride I 123 (IMP) with single photon emission computed tomography in Alzheimer's disease, we studied 58 patients with AD and 15 age-matched healthy control subjects. We used a qualitative method to assess regional IMP uptake in the entire brain and to rate image data sets as normal or abnormal without knowledge of subjects'clinical classification. The sensitivity and specificity of IMP with single photon emission computed tomography in AD were 88% and 87%, respectively. In 15 patients with mild cognitive deficits (Blessed Dementia Scale score, less than or equal to 10), sensitivity was 80%. With the use of a semiquantitative measure of regional cortical IMP uptake, the parietal lobes were the most functionally impaired in AD and the most strongly associated with the patients' Blessed Dementia Scale scores. These results indicated that IMP with single photon emission computed tomography may be a useful adjunct in the clinical diagnosis of AD in early, mild disease.
Necessary conditions for accurate computations of three-body partial decay widths
NASA Astrophysics Data System (ADS)
Garrido, E.; Jensen, A. S.; Fedorov, D. V.
2008-09-01
The partial width for decay of a resonance into three fragments is largely determined at distances where the energy is smaller than the effective potential producing the corresponding wave function. At short distances the many-body properties are accounted for by preformation or spectroscopic factors. We use the adiabatic expansion method combined with the WKB approximation to obtain the indispensable cluster model wave functions at intermediate and larger distances. We test the concept by deriving conditions for the minimal basis expressed in terms of partial waves and radial nodes. We compare results for different effective interactions and methods. Agreement is found with experimental values for a sufficiently large basis. We illustrate the ideas with realistic examples from α emission of C12 and two-proton emission of Ne17. Basis requirements for accurate momentum distributions are briefly discussed.
A mechanistic approach for accurate simulation of village scale malaria transmission
Bomblies, Arne; Duchemin, Jean-Bernard; Eltahir, Elfatih AB
2009-01-01
Background Malaria transmission models commonly incorporate spatial environmental and climate variability for making regional predictions of disease risk. However, a mismatch of these models' typical spatial resolutions and the characteristic scale of malaria vector population dynamics may confound disease risk predictions in areas of high spatial hydrological variability such as the Sahel region of Africa. Methods Field observations spanning two years from two Niger villages are compared. The two villages are separated by only 30 km but exhibit a ten-fold difference in anopheles mosquito density. These two villages would be covered by a single grid cell in many malaria models, yet their entomological activity differs greatly. Environmental conditions and associated entomological activity are simulated at high spatial- and temporal resolution using a mechanistic approach that couples a distributed hydrology scheme and an entomological model. Model results are compared to regular field observations of Anopheles gambiae sensu lato mosquito populations and local hydrology. The model resolves the formation and persistence of individual pools that facilitate mosquito breeding and predicts spatio-temporal mosquito population variability at high resolution using an agent-based modeling approach. Results Observations of soil moisture, pool size, and pool persistence are reproduced by the model. The resulting breeding of mosquitoes in the simulated pools yields time-integrated seasonal mosquito population dynamics that closely follow observations from captured mosquito abundance. Interannual difference in mosquito abundance is simulated, and the inter-village difference in mosquito population is reproduced for two years of observations. These modeling results emulate the known focal nature of malaria in Niger Sahel villages. Conclusion Hydrological variability must be represented at high spatial and temporal resolution to achieve accurate predictive ability of malaria risk
A novel approach for accurate radiative transfer in cosmological hydrodynamic simulations
NASA Astrophysics Data System (ADS)
Petkova, Margarita; Springel, Volker
2011-08-01
We present a numerical implementation of radiative transfer based on an explicitly photon-conserving advection scheme, where radiative fluxes over the cell interfaces of a structured or unstructured mesh are calculated with a second-order reconstruction of the intensity field. The approach employs a direct discretization of the radiative transfer equation in Boltzmann form with adjustable angular resolution that, in principle, works equally well in the optically-thin and optically-thick regimes. In our most general formulation of the scheme, the local radiation field is decomposed into a linear sum of directional bins of equal solid angle, tessellating the unit sphere. Each of these 'cone fields' is transported independently, with constant intensity as a function of the direction within the cone. Photons propagate at the speed of light (or optionally using a reduced speed of light approximation to allow larger time-steps), yielding a fully time-dependent solution of the radiative transfer equation that can naturally cope with an arbitrary number of sources, as well as with scattering. The method casts sharp shadows, subject to the limitations induced by the adopted angular resolution. If the number of point sources is small and scattering is unimportant, our implementation can alternatively treat each source exactly in angular space, producing shadows whose sharpness is only limited by the grid resolution. A third hybrid alternative is to treat only a small number of the locally most luminous point sources explicitly, with the rest of the radiation intensity followed in a radiative diffusion approximation. We have implemented the method in the moving-mesh code AREPO, where it is coupled to the hydrodynamics in an operator-splitting approach that subcycles the radiative transfer alternately with the hydrodynamical evolution steps. We also discuss our treatment of basic photon sink processes relevant to cosmological reionization, with a chemical network that can
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-31
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4) Ha/Bohr.
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10^{-4} Ha/Bohr.
NASA Astrophysics Data System (ADS)
Alexandre, E.; Cuadra, L.; Nieto-Borge, J. C.; Candil-García, G.; del Pino, M.; Salcedo-Sanz, S.
2015-08-01
Wave parameters computed from time series measured by buoys (significant wave height Hs, mean wave period, etc.) play a key role in coastal engineering and in the design and operation of wave energy converters. Storms or navigation accidents can make measuring buoys break down, leading to missing data gaps. In this paper we tackle the problem of locally reconstructing Hs at out-of-operation buoys by using wave parameters from nearby buoys, based on the spatial correlation among values at neighboring buoy locations. The novelty of our approach for its potential application to problems in coastal engineering is twofold. On one hand, we propose a genetic algorithm hybridized with an extreme learning machine that selects, among the available wave parameters from the nearby buoys, a subset FnSP with nSP parameters that minimizes the Hs reconstruction error. On the other hand, we evaluate to what extent the selected parameters in subset FnSP are good enough in assisting other machine learning (ML) regressors (extreme learning machines, support vector machines and gaussian process regression) to reconstruct Hs. The results show that all the ML method explored achieve a good Hs reconstruction in the two different locations studied (Caribbean Sea and West Atlantic).
NASA Astrophysics Data System (ADS)
Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.
2013-12-01
This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.
NASA Astrophysics Data System (ADS)
Bellouard, Yves; Sulzmann, Armin; Jacot, Jacques; Clavel, Reymond
1998-01-01
In the robotics field, several grippers have been developed using SMA technologies, but, so far, SMA is only used as the actuating part of the mechanical device. However mechanical device requires assembly and in some cases this means friction. In the case of micro-grippers, this becomes a major problem due to the small size of the components. In this paper, a new monolithic concept of micro-gripper is presented. This concept is applied to the grasping of sub- millimeter optical elements such as Selfoc lenses and the fastening of optical fibers. Measurements are performed using a newly developed high precision 3D-computer vision tracking system to characterize the spatial positions of the micro-gripper in action. To characterize relative motion of the micro-gripper the natural texture of the micro-gripper is used to compute 3D displacement. The microscope image CCD receivers high frequency changes in light intensity from the surface of the ripper. Using high resolution camera calibration, passive auto focus algorithms and 2D object recognition, the position of the micro-gripper can be characterized in the 3D workspace and can be guided in future micro assembly tasks.
Accurate quantification of width and density of bone structures by computed tomography
Hangartner, Thomas N.; Short, David F.
2007-10-15
In computed tomography (CT), the representation of edges between objects of different densities is influenced by the limited spatial resolution of the scanner. This results in the misrepresentation of density of narrow objects, leading to errors of up to 70% and more. Our interest is in the imaging and measurement of narrow bone structures, and the issues are the same for imaging with clinical CT scanners, peripheral quantitative CT scanners or micro CT scanners. Mathematical models, phantoms and tests with patient data led to the following procedures: (i) extract density profiles at one-degree increments from the CT images at right angles to the bone boundary; (ii) consider the outer and inner edge of each profile separately due to different adjacent soft tissues; (iii) measure the width of each profile based on a threshold at fixed percentage of the difference between the soft-tissue value and a first approximated bone value; (iv) correct the underlying material density of bone for each profile based on the measured width with the help of the density-versus-width curve obtained from computer simulations and phantom measurements. This latter curve is specific to a certain scanner and is not dependent on the densities of the tissues within the range seen in patients. This procedure allows the calculation of the material density of bone. Based on phantom measurements, we estimate the density error to be below 2% relative to the density of normal bone and the bone-width error about one tenth of a pixel size.
A computational approach to negative priming
NASA Astrophysics Data System (ADS)
Schrobsdorff, H.; Ihrke, M.; Kabisch, B.; Behrendt, J.; Hasselhorn, M.; Herrmann, J. Michael
2007-09-01
Priming is characterized by a sensitivity of reaction times to the sequence of stimuli in psychophysical experiments. The reduction of the reaction time observed in positive priming is well-known and experimentally understood (Scarborough et al., J. Exp. Psycholol: Hum. Percept. Perform., 3, pp. 1-17, 1977). Negative priming—the opposite effect—is experimentally less tangible (Fox, Psychonom. Bull. Rev., 2, pp. 145-173, 1995). The dependence on subtle parameter changes (such as response-stimulus interval) usually varies. The sensitivity of the negative priming effect bears great potential for applications in research in fields such as memory, selective attention, and ageing effects. We develop and analyse a computational realization, CISAM, of a recent psychological model for action decision making, the ISAM (Kabisch, PhD thesis, Friedrich-Schiller-Universitat, 2003), which is sensitive to priming conditions. With the dynamical systems approach of the CISAM, we show that a single adaptive threshold mechanism is sufficient to explain both positive and negative priming effects. This is achieved by comparing results obtained by the computational modelling with experimental data from our laboratory. The implementation provides a rich base from which testable predictions can be derived, e.g. with respect to hitherto untested stimulus combinations (e.g. single-object trials).
NEW APPROACHES: Using a computer to graphically illustrate equipotential lines
NASA Astrophysics Data System (ADS)
Phongdara, Boonlua
1998-09-01
A simple mathematical model and computer program allow students to plot equipotential lines, for example for two terminals in a tank of water, in a way that is easier and faster but just as accurate as the traditional method.
A novel class of highly efficient and accurate time-integrators in nonlinear computational mechanics
NASA Astrophysics Data System (ADS)
Wang, Xuechuan; Atluri, Satya N.
2017-01-01
A new class of time-integrators is presented for strongly nonlinear dynamical systems. These algorithms are far superior to the currently common time integrators in computational efficiency and accuracy. These three algorithms are based on a local variational iteration method applied over a finite interval of time. By using Chebyshev polynomials as trial functions and Dirac-Delta functions as the test functions over the finite time interval, the three algorithms are developed into three different discrete time-integrators through the collocation method. These time integrators are labeled as Chebyshev local iterative collocation methods. Through examples of the forced Duffing oscillator, the Lorenz system, and the multiple coupled Duffing equations (which arise as semi-discrete equations for beams, plates and shells undergoing large deformations), it is shown that the new algorithms are far superior to the 4th order Runge-Kutta and ODE45 of MATLAB, in predicting the chaotic responses of strongly nonlinear dynamical systems.
NASA Technical Reports Server (NTRS)
Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)
2008-01-01
A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.
Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals' Behaviour.
Barnard, Shanis; Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola
2016-01-01
Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs' behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals' quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog's shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non
Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals’ Behaviour
Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola
2016-01-01
Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs’ behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals’ quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog’s shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non
NASA Astrophysics Data System (ADS)
Henniger, R.; Obrist, D.; Kleiser, L.
2010-05-01
The emergence of "petascale" supercomputers requires us to develop today's simulation codes for (incompressible) flows by codes which are using numerical schemes and methods that are better able to exploit the offered computational power. In that spirit, we present a massively parallel high-order Navier-Stokes solver for large incompressible flow problems in three dimensions. The governing equations are discretized with finite differences in space and a semi-implicit time integration scheme. This discretization leads to a large linear system of equations which is solved with a cascade of iterative solvers. The iterative solver for the pressure uses a highly efficient commutation-based preconditioner which is robust with respect to grid stretching. The efficiency of the implementation is further enhanced by carefully setting the (adaptive) termination criteria for the different iterative solvers. The computational work is distributed to different processing units by a geometric data decomposition in all three dimensions. This decomposition scheme ensures a low communication overhead and excellent scaling capabilities. The discretization is thoroughly validated. First, we verify the convergence orders of the spatial and temporal discretizations for a forced channel flow. Second, we analyze the iterative solution technique by investigating the absolute accuracy of the implementation with respect to the different termination criteria. Third, Orr-Sommerfeld and Squire eigenmodes for plane Poiseuille flow are simulated and compared to analytical results. Fourth, the practical applicability of the implementation is tested for transitional and turbulent channel flow. The results are compared to solutions from a pseudospectral solver. Subsequently, the performance of the commutation-based preconditioner for the pressure iteration is demonstrated. Finally, the excellent parallel scalability of the proposed method is demonstrated with a weak and a strong scaling test on up to
Time-Accurate Computational Fluid Dynamics Simulation of a Pair of Moving Solid Rocket Boosters
NASA Technical Reports Server (NTRS)
Strutzenberg, Louise L.; Williams, Brandon R.
2011-01-01
Since the Columbia accident, the threat to the Shuttle launch vehicle from debris during the liftoff timeframe has been assessed by the Liftoff Debris Team at NASA/MSFC. In addition to engineering methods of analysis, CFD-generated flow fields during the liftoff timeframe have been used in conjunction with 3-DOF debris transport methods to predict the motion of liftoff debris. Early models made use of a quasi-steady flow field approximation with the vehicle positioned at a fixed location relative to the ground; however, a moving overset mesh capability has recently been developed for the Loci/CHEM CFD software which enables higher-fidelity simulation of the Shuttle transient plume startup and liftoff environment. The present work details the simulation of the launch pad and mobile launch platform (MLP) with truncated solid rocket boosters (SRBs) moving in a prescribed liftoff trajectory derived from Shuttle flight measurements. Using Loci/CHEM, time-accurate RANS and hybrid RANS/LES simulations were performed for the timeframe T0+0 to T0+3.5 seconds, which consists of SRB startup to a vehicle altitude of approximately 90 feet above the MLP. Analysis of the transient flowfield focuses on the evolution of the SRB plumes in the MLP plume holes and the flame trench, impingement on the flame deflector, and especially impingment on the MLP deck resulting in upward flow which is a transport mechanism for debris. The results show excellent qualitative agreement with the visual record from past Shuttle flights, and comparisons to pressure measurements in the flame trench and on the MLP provide confidence in these simulation capabilities.
Time-Accurate Incompressible Navier-Stokes Computations with Overlapped Moving Grids
NASA Technical Reports Server (NTRS)
Kiris, Cetin; Kwak, Dochan; Rogers, Stuart; Lee, Yu-Tai; Kutler, Paul (Technical Monitor)
1994-01-01
MIT flapping foil experiment was used as a validation case to evaluate the current incompressible Navier-Stokes approach with overlapped grid schemes. Steady-state calculations were carried out for overlapped and patched grids. The grid dependency, turbulence model effects, and the effect of order of differencing were investigated. Numerical results were compared against experimental data. The resulting procedure were applied to unsteady flapping foil calculations. Two upstream NACA 0025 foils perform high-frequency synchronized motion and generate unsteady flow conditions to the downstream larger stationary foil. Comparison between unsteady experimental data and numerical results from two different moving boundary procedures will be presented.
Computational approaches to predict bacteriophage-host relationships.
Edwards, Robert A; McNair, Katelyn; Faust, Karoline; Raes, Jeroen; Dutilh, Bas E
2016-03-01
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage-host relationships, with potential relevance for medical and industrial applications.
Accurate Computed Enthalpies of Spin Crossover in Iron and Cobalt Complexes
NASA Astrophysics Data System (ADS)
Jensen, Kasper P.; Cirera, Jordi
2009-08-01
Despite their importance in many chemical processes, the relative energies of spin states of transition metal complexes have so far been haunted by large computational errors. By the use of six functionals, B3LYP, BP86, TPSS, TPSSh, M06, and M06L, this work studies nine complexes (seven with iron and two with cobalt) for which experimental enthalpies of spin crossover are available. It is shown that such enthalpies can be used as quantitative benchmarks of a functional's ability to balance electron correlation in both the involved states. TPSSh achieves an unprecedented mean absolute error of ˜11 kJ/mol in spin transition energies, with the local functional M06L a distant second (25 kJ/mol). Other tested functionals give mean absolute errors of 40 kJ/mol or more. This work confirms earlier suggestions that 10% exact exchange is near-optimal for describing the electron correlation effects of first-row transition metal systems. Furthermore, it is shown that given an experimental structure of an iron complex, TPSSh can predict the electronic state corresponding to that experimental structure. We recommend this functional as current state-of-the-art for studying spin crossover and relative energies of close-lying electronic configurations in first-row transition metal systems.
Li, Xin; Han, Xingpeng; Sun, Wei; Wang, Meng; Jing, Guohui
2016-01-01
Background To evaluate the role of computed tomography (CT) in preoperative diagnosis of intrathymic cyst and small thymoma, and determine the best CT threshold for distinguish intrathymic cyst from small thymoma. Methods We retrospectively reviewed the medical records of 30 patients (17 intrathymic cyst and 13 small thymoma) who had undergone mediastinal masses resection (with diameter less than 3 cm) under thoracoscope between January 2014 and July 2015 at our hospital. Clinical and CT features were compared and receiver-operating characteristics curve (ROC) analysis was performed. Results The CT value of small thymoma [39.5 HU (IQR, 33.7–42.2 HU)] was significantly higher than intrathymic cyst [25.8 HU (IQR, 22.3–29.3 HU), P=0.004]. When CT value was 31.2 HU, it could act as a threshold for identification of small thymoma and intrathymic cyst (the sensitivity and specificity was 92.3% and 82.4%, respectively). The ΔCT value of enhanced CT value with the non-enhanced CT value was significantly different between small thymoma [18.7 HU (IQR, 10.9–19.0 HU)] and intrathymic cyst [4.3 HU (IQR, 3.0–11.7 HU), P=0.04]. The density was more homogenous in intrathymic cyst than small thymoma, and the contour of the intrathymic cyst was more smoothly than small thymoma. Conclusions Preoperative CT scans could help clinicians to identify intrathymic cyst and small thymoma, and we recommend 31.2 HU as the best thresholds. Contrast-enhanced CT scans is useful for further identification of the two diseases. PMID:27621863
Vela, Sergi; Fumanal, Maria; Ribas-Arino, Jordi; Robert, Vincent
2015-07-07
The DFT + U methodology is regarded as one of the most-promising strategies to treat the solid state of molecular materials, as it may provide good energetic accuracy at a moderate computational cost. However, a careful parametrization of the U-term is mandatory since the results may be dramatically affected by the selected value. Herein, we benchmarked the Hubbard-like U-term for seven Fe(ii)N6-based pseudo-octahedral spin crossover (SCO) compounds, using as a reference an estimation of the electronic enthalpy difference (ΔHelec) extracted from experimental data (T1/2, ΔS and ΔH). The parametrized U-value obtained for each of those seven compounds ranges from 2.37 eV to 2.97 eV, with an average value of U = 2.65 eV. Interestingly, we have found that this average value can be taken as a good starting point since it leads to an unprecedented mean absolute error (MAE) of only 4.3 kJ mol(-1) in the evaluation of ΔHelec for the studied compounds. Moreover, by comparing our results on the solid state and the gas phase of the materials, we quantify the influence of the intermolecular interactions on the relative stability of the HS and LS states, with an average effect of ca. 5 kJ mol(-1), whose sign cannot be generalized. Overall, the findings reported in this manuscript pave the way for future studies devoted to understand the crystalline phase of SCO compounds, or the adsorption of individual molecules on organic or metallic surfaces, in which the rational incorporation of the U-term within DFT + U yields the required energetic accuracy that is dramatically missing when using bare-DFT functionals.
NASA Astrophysics Data System (ADS)
Hrubý, Jan
2012-04-01
Mathematical modeling of the non-equilibrium condensing transonic steam flow in the complex 3D geometry of a steam turbine is a demanding problem both concerning the physical concepts and the required computational power. Available accurate formulations of steam properties IAPWS-95 and IAPWS-IF97 require much computation time. For this reason, the modelers often accept the unrealistic ideal-gas behavior. Here we present a computation scheme based on a piecewise, thermodynamically consistent representation of the IAPWS-95 formulation. Density and internal energy are chosen as independent variables to avoid variable transformations and iterations. On the contrary to the previous Tabular Taylor Series Expansion Method, the pressure and temperature are continuous functions of the independent variables, which is a desirable property for the solution of the differential equations of the mass, energy, and momentum conservation for both phases.
NASA Astrophysics Data System (ADS)
Yi, Sha-Sha; Pan, Cong; Hu, Zhong-Han
2015-12-01
Modern computer simulations of biological systems often involve an explicit treatment of the complex interactions among a large number of molecules. While it is straightforward to compute the short-ranged Van der Waals interaction in classical molecular dynamics simulations, it has been a long-lasting issue to develop accurate methods for the longranged Coulomb interaction. In this short review, we discuss three types of methodologies for the accurate treatment of electrostatics in simulations of explicit molecules: truncation-type methods, Ewald-type methods, and mean-field-type methods. Throughout the discussion, we brief the formulations and developments of these methods, emphasize the intrinsic connections among the three types of methods, and focus on the existing problems which are often associated with the boundary conditions of electrostatics. This brief survey is summarized with a short perspective on future trends along the method developments and applications in the field of biological simulations. Project supported by the National Natural Science Foundation of China (Grant Nos. 91127015 and 21522304) and the Open Project from the State Key Laboratory of Theoretical Physics, and the Innovation Project from the State Key Laboratory of Supramolecular Structure and Materials.
Manz, Thomas A; Sholl, David S
2011-12-13
The partitioning of electron spin density among atoms in a material gives atomic spin moments (ASMs), which are important for understanding magnetic properties. We compare ASMs computed using different population analysis methods and introduce a method for computing density derived electrostatic and chemical (DDEC) ASMs. Bader and DDEC ASMs can be computed for periodic and nonperiodic materials with either collinear or noncollinear magnetism, while natural population analysis (NPA) ASMs can be computed for nonperiodic materials with collinear magnetism. Our results show Bader, DDEC, and (where applicable) NPA methods give similar ASMs, but different net atomic charges. Because they are optimized to reproduce both the magnetic field and the chemical states of atoms in a material, DDEC ASMs are especially suitable for constructing interaction potentials for atomistic simulations. We describe the computation of accurate ASMs for (a) a variety of systems using collinear and noncollinear spin DFT, (b) highly correlated materials (e.g., magnetite) using DFT+U, and (c) various spin states of ozone using coupled cluster expansions. The computed ASMs are in good agreement with available experimental results for a variety of periodic and nonperiodic materials. Examples considered include the antiferromagnetic metal organic framework Cu3(BTC)2, several ozone spin states, mono- and binuclear transition metal complexes, ferri- and ferro-magnetic solids (e.g., Fe3O4, Fe3Si), and simple molecular systems. We briefly discuss the theory of exchange-correlation functionals for studying noncollinear magnetism. A method for finding the ground state of systems with highly noncollinear magnetism is introduced. We use these methods to study the spin-orbit coupling potential energy surface of the single molecule magnet Fe4C40H52N4O12, which has highly noncollinear magnetism, and find that it contains unusual features that give a new interpretation to experimental data.
Computer Metaphors: Approaches to Computer Literacy for Educators.
ERIC Educational Resources Information Center
Peelle, Howard A.
Because metaphors offer ready perspectives for comprehending something new, this document examines various metaphors educators might use to help students develop computer literacy. Metaphors described are the computer as person (a complex system worthy of respect), tool (perhaps the most powerful and versatile known to humankind), brain (both…
NASA Technical Reports Server (NTRS)
Kory, Carol L.
1999-01-01
The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made
Zhang, Jun; Dolg, Michael
2013-07-09
An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.
Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing
NASA Technical Reports Server (NTRS)
Kory, Carol L.
2001-01-01
The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be
Accurate Vehicle Location System Using RFID, an Internet of Things Approach.
Prinsloo, Jaco; Malekian, Reza
2016-06-04
Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved.
Accurate Vehicle Location System Using RFID, an Internet of Things Approach
Prinsloo, Jaco; Malekian, Reza
2016-01-01
Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved. PMID:27271638
Fast and Accurate Electronic Excitations in Cyanines with the Many-Body Bethe-Salpeter Approach.
Boulanger, Paul; Jacquemin, Denis; Duchemin, Ivan; Blase, Xavier
2014-03-11
The accurate prediction of the optical signatures of cyanine derivatives remains an important challenge in theoretical chemistry. Indeed, up to now, only the most expensive quantum chemical methods (CAS-PT2, CC, DMC, etc.) yield consistent and accurate data, impeding the applications on real-life molecules. Here, we investigate the lowest lying singlet excitation energies of increasingly long cyanine dyes within the GW and Bethe-Salpeter Green's function many-body perturbation theory. Our results are in remarkable agreement with available coupled-cluster (exCC3) data, bringing these two single-reference perturbation techniques within a 0.05 eV maximum discrepancy. By comparison, available TD-DFT calculations with various semilocal, global, or range-separated hybrid functionals, overshoot the transition energies by a typical error of 0.3-0.6 eV. The obtained accuracy is achieved with a parameter-free formalism that offers similar accuracy for metallic or insulating, finite size or extended systems.
Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo
2015-01-01
A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116
Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes.
Dang, Na Le; Hughes, Tyler B; Miller, Grover P; Swamidass, S Joshua
2017-03-14
Structural alerts are commonly used in drug discovery to identify molecules likely to form reactive metabolites and thereby become toxic. Unfortunately, as useful as structural alerts are, they do not effectively model if, when, and why metabolism renders safe molecules toxic. Toxicity due to a specific structural alert is highly conditional, depending on the metabolism of the alert, the reactivity of its metabolites, dosage, and competing detoxification pathways. A systems approach, which explicitly models these pathways, could more effectively assess the toxicity risk of drug candidates. In this study, we demonstrated that mathematical models of P450 metabolism can predict the context-specific probability that a structural alert will be bioactivated in a given molecule. This study focuses on the furan, phenol, nitroaromatic, and thiophene alerts. Each of these structural alerts can produce reactive metabolites through certain metabolic pathways but not always. We tested whether our metabolism modeling approach, XenoSite, can predict when a given molecule's alerts will be bioactivated. Specifically, we used models of epoxidation, quinone formation, reduction, and sulfur-oxidation to predict the bioactivation of furan-, phenol-, nitroaromatic-, and thiophene-containing drugs. Our models separated bioactivated and not-bioactivated furan-, phenol-, nitroaromatic-, and thiophene-containing drugs with AUC performances of 100%, 73%, 93%, and 88%, respectively. Metabolism models accurately predict whether alerts are bioactivated and thus serve as a practical approach to improve the interpretability and usefulness of structural alerts. We expect that this same computational approach can be extended to most other structural alerts and later integrated into toxicity risk models. This advance is one necessary step toward our long-term goal of building comprehensive metabolic models of bioactivation and detoxification to guide assessment and design of new therapeutic
Digital test signal generation: An accurate SNR calibration approach for the DSN
NASA Technical Reports Server (NTRS)
Gutierrez-Luaces, B. O.
1991-01-01
A new method of generating analog test signals with accurate signal to noise ratios (SNRs) is described. High accuracy will be obtained by simultaneous generation of digital noise and signal spectra at a given baseband or bandpass limited bandwidth. The digital synthesis will provide a test signal embedded in noise with the statistical properties of a stationary random process. Accuracy will only be dependent on test integration time with a limit imposed by the system quantization noise (expected to be 0.02 dB). Setability will be approximately 0.1 dB. The first digital SNR generator to provide baseband test signals is being built and will be available in early 1991.
Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti
2016-01-07
The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.
Simple and surprisingly accurate approach to the chemical bond obtained from dimensional scaling.
Svidzinsky, Anatoly A; Scully, Marlan O; Herschbach, Dudley R
2005-08-19
We present a new dimensional scaling transformation of the Schrödinger equation for the two electron bond. This yields, for the first time, a good description of the bond via D scaling. There also emerges, in the large-D limit, an intuitively appealing semiclassical picture, akin to a molecular model proposed by Bohr in 1913. In this limit, the electrons are confined to specific orbits in the scaled space, yet the uncertainty principle is maintained. A first-order perturbation correction, proportional to 1/D, substantially improves the agreement with the exact ground state potential energy curve. The present treatment is very simple mathematically, yet provides a strikingly accurate description of the potential curves for the lowest singlet, triplet, and excited states of H2. We find the modified D-scaling method also gives good results for other molecules. It can be combined advantageously with Hartree-Fock and other conventional methods.
Dynamical Approach Study of Spurious Numerics in Nonlinear Computations
NASA Technical Reports Server (NTRS)
Yee, H. C.; Mansour, Nagi (Technical Monitor)
2002-01-01
The last two decades have been an era when computation is ahead of analysis and when very large scale practical computations are increasingly used in poorly understood multiscale complex nonlinear physical problems and non-traditional fields. Ensuring a higher level of confidence in the predictability and reliability (PAR) of these numerical simulations could play a major role in furthering the design, understanding, affordability and safety of our next generation air and space transportation systems, and systems for planetary and atmospheric sciences, and in understanding the evolution and origin of life. The need to guarantee PAR becomes acute when computations offer the ONLY way of solving these types of data limited problems. Employing theory from nonlinear dynamical systems, some building blocks to ensure a higher level of confidence in PAR of numerical simulations have been revealed by the author and world expert collaborators in relevant fields. Five building blocks with supporting numerical examples were discussed. The next step is to utilize knowledge gained by including nonlinear dynamics, bifurcation and chaos theories as an integral part of the numerical process. The third step is to design integrated criteria for reliable and accurate algorithms that cater to the different multiscale nonlinear physics. This includes but is not limited to the construction of appropriate adaptive spatial and temporal discretizations that are suitable for the underlying governing equations. In addition, a multiresolution wavelets approach for adaptive numerical dissipation/filter controls for high speed turbulence, acoustics and combustion simulations will be sought. These steps are corner stones for guarding against spurious numerical solutions that are solutions of the discretized counterparts but are not solutions of the underlying governing equations.
Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach
Zimmer, Jennifer S.D.; Monroe, Matthew E.; Qian, Wei-Jun; Smith, Richard D.
2007-01-01
Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. PMID:16429408
Meng, Qingyong; Chen, Jun; Zhang, Dong H
2016-04-21
To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ∼20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2016-04-01
To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.
Adde, Lars; Helbostad, Jorunn; Jensenius, Alexander R; Langaas, Mette; Støen, Ragnhild
2013-08-01
This study evaluates the role of postterm age at assessment and the use of one or two video recordings for the detection of fidgety movements (FMs) and prediction of cerebral palsy (CP) using computer vision software. Recordings between 9 and 17 weeks postterm age from 52 preterm and term infants (24 boys, 28 girls; 26 born preterm) were used. Recordings were analyzed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analysis. Sensitivities, specificities, and area under curve were estimated for the first and second recording, or a mean of both. FMs were classified based on the Prechtl approach of general movement assessment. CP status was reported at 2 years. Nine children developed CP of whom all recordings had absent FMs. The mean variability of the centroid of motion (CSD) from two recordings was more accurate than using only one recording, and identified all children who were diagnosed with CP at 2 years. Age at assessment did not influence the detection of FMs or prediction of CP. The accuracy of computer vision techniques in identifying FMs and predicting CP based on two recordings should be confirmed in future studies.
An Accurate and Generic Testing Approach to Vehicle Stability Parameters Based on GPS and INS
Miao, Zhibin; Zhang, Hongtian; Zhang, Jinzhu
2015-01-01
With the development of the vehicle industry, controlling stability has become more and more important. Techniques of evaluating vehicle stability are in high demand. As a common method, usually GPS sensors and INS sensors are applied to measure vehicle stability parameters by fusing data from the two system sensors. Although prior model parameters should be recognized in a Kalman filter, it is usually used to fuse data from multi-sensors. In this paper, a robust, intelligent and precise method to the measurement of vehicle stability is proposed. First, a fuzzy interpolation method is proposed, along with a four-wheel vehicle dynamic model. Second, a two-stage Kalman filter, which fuses the data from GPS and INS, is established. Next, this approach is applied to a case study vehicle to measure yaw rate and sideslip angle. The results show the advantages of the approach. Finally, a simulation and real experiment is made to verify the advantages of this approach. The experimental results showed the merits of this method for measuring vehicle stability, and the approach can meet the design requirements of a vehicle stability controller. PMID:26690154
A stationary wavelet entropy-based clustering approach accurately predicts gene expression.
Nguyen, Nha; Vo, An; Choi, Inchan; Won, Kyoung-Jae
2015-03-01
Studying epigenetic landscapes is important to understand the condition for gene regulation. Clustering is a useful approach to study epigenetic landscapes by grouping genes based on their epigenetic conditions. However, classical clustering approaches that often use a representative value of the signals in a fixed-sized window do not fully use the information written in the epigenetic landscapes. Clustering approaches to maximize the information of the epigenetic signals are necessary for better understanding gene regulatory environments. For effective clustering of multidimensional epigenetic signals, we developed a method called Dewer, which uses the entropy of stationary wavelet of epigenetic signals inside enriched regions for gene clustering. Interestingly, the gene expression levels were highly correlated with the entropy levels of epigenetic signals. Dewer separates genes better than a window-based approach in the assessment using gene expression and achieved a correlation coefficient above 0.9 without using any training procedure. Our results show that the changes of the epigenetic signals are useful to study gene regulation.
An Accurate and Generic Testing Approach to Vehicle Stability Parameters Based on GPS and INS.
Miao, Zhibin; Zhang, Hongtian; Zhang, Jinzhu
2015-12-04
With the development of the vehicle industry, controlling stability has become more and more important. Techniques of evaluating vehicle stability are in high demand. As a common method, usually GPS sensors and INS sensors are applied to measure vehicle stability parameters by fusing data from the two system sensors. Although prior model parameters should be recognized in a Kalman filter, it is usually used to fuse data from multi-sensors. In this paper, a robust, intelligent and precise method to the measurement of vehicle stability is proposed. First, a fuzzy interpolation method is proposed, along with a four-wheel vehicle dynamic model. Second, a two-stage Kalman filter, which fuses the data from GPS and INS, is established. Next, this approach is applied to a case study vehicle to measure yaw rate and sideslip angle. The results show the advantages of the approach. Finally, a simulation and real experiment is made to verify the advantages of this approach. The experimental results showed the merits of this method for measuring vehicle stability, and the approach can meet the design requirements of a vehicle stability controller.
A morphometric approach for the accurate solvation thermodynamics of proteins and ligands.
Harano, Yuichi; Roth, Roland; Chiba, Shuntaro
2013-09-05
We have developed a versatile method for calculating solvation thermodynamic quantities for molecules, starting from their atomic coordinates. The contribution of each atom to the thermodynamic quantities is estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem, and the coefficients reflecting their solvation properties. This treatment enables us to calculate the solvation free energy with high accuracy despite of the limited computational load. The method can readily be applied to macromolecules in an all-atom molecular model, allowing the stability of these molecules' structures in solution to be evaluated.
Xiang, G.; Ferson, S.; Ginzburg, L.; Longpré, L.; Mayorga, E.; Kosheleva, O.
2013-01-01
To preserve privacy, the original data points (with exact values) are replaced by boxes containing each (inaccessible) data point. This privacy-motivated uncertainty leads to uncertainty in the statistical characteristics computed based on this data. In a previous paper, we described how to minimize this uncertainty under the assumption that we use the same standard statistical estimates for the desired characteristics. In this paper, we show that we can further decrease the resulting uncertainty if we allow fuzzy-motivated weighted estimates, and we explain how to optimally select the corresponding weights. PMID:25187183
Computational dynamics for robotics systems using a non-strict computational approach
NASA Technical Reports Server (NTRS)
Orin, David E.; Wong, Ho-Cheung; Sadayappan, P.
1989-01-01
A Non-Strict computational approach for real-time robotics control computations is proposed. In contrast to the traditional approach to scheduling such computations, based strictly on task dependence relations, the proposed approach relaxes precedence constraints and scheduling is guided instead by the relative sensitivity of the outputs with respect to the various paths in the task graph. An example of the computation of the Inverse Dynamics of a simple inverted pendulum is used to demonstrate the reduction in effective computational latency through use of the Non-Strict approach. A speedup of 5 has been obtained when the processes of the task graph are scheduled to reduce the latency along the crucial path of the computation. While error is introduced by the relaxation of precedence constraints, the Non-Strict approach has a smaller error than the conventional Strict approach for a wide range of input conditions.
Baiardi, Alberto; Bloino, Julien; Barone, Vincenzo
2015-07-14
The interpretation and analysis of experimental resonance-Raman (RR) spectra can be significantly facilitated by vibronic computations based on reliable quantum-mechanical (QM) methods. With the aim of improving the description of large and flexible molecules, our recent time-dependent formulation to compute vibrationally resolved electronic spectra, based on Cartesian coordinates, has been extended to support internal coordinates. A set of nonredundant delocalized coordinates is automatically generated from the molecular connectivity thanks to a new general and robust procedure. In order to validate our implementation, a series of molecules has been used as test cases. Among them, rigid systems show that normal modes based on Cartesian and delocalized internal coordinates provide equivalent results, but the latter set is much more convenient and reliable for systems characterized by strong geometric deformations associated with the electronic transition. The so-called Z-matrix internal coordinates, which perform well for chain molecules, are also shown to be poorly suited in the presence of cycles or nonstandard structures.
Accurate Waveforms for Non-spinning Binary Black Holes using the Effective-one-body Approach
NASA Technical Reports Server (NTRS)
Buonanno, Alessandra; Pan, Yi; Baker, John G.; Centrella, Joan; Kelly, Bernard J.; McWilliams, Sean T.; vanMeter, James R.
2007-01-01
Using numerical relativity as guidance and the natural flexibility of the effective-one-body (EOB) model, we extend the latter so that it can successfully match the numerical relativity waveforms of non-spinning binary black holes during the last stages of inspiral, merger and ringdown. Here, by successfully, we mean with phase differences < or approx. 8% of a gravitational-wave cycle accumulated until the end of the ringdown phase. We obtain this result by simply adding a 4 post-Newtonian order correction in the EOB radial potential and determining the (constant) coefficient by imposing high-matching performances with numerical waveforms of mass ratios m1/m2 = 1,2/3,1/2 and = 1/4, m1 and m2 being the individual black-hole masses. The final black-hole mass and spin predicted by the numerical simulations are used to determine the ringdown frequency and decay time of three quasi-normal-mode damped sinusoids that are attached to the EOB inspiral-(plunge) waveform at the light-ring. The accurate EOB waveforms may be employed for coherent searches of gravitational waves emitted by non-spinning coalescing binary black holes with ground-based laser-interferometer detectors.
Accurate characterization of weak neutron fields by using a Bayesian approach.
Medkour Ishak-Boushaki, G; Allab, M
2017-04-01
A Bayesian analysis of data derived from neutron spectrometric measurements provides the advantage of determining rigorously integral physical quantities characterizing the neutron field and their respective related uncertainties. The first and essential step in a Bayesian approach is the parameterization of the investigated neutron spectrum. The aim of this paper is to investigate the sensitivity of the Bayesian results, mainly the neutron dose H(*)(10) required for radiation protection purposes and its correlated uncertainty, to the selected neutron spectrum parameterization.
Effective approach for accurately calculating individual energy of polar heterojunction interfaces
NASA Astrophysics Data System (ADS)
Akiyama, Toru; Nakane, Harunobu; Nakamura, Kohji; Ito, Tomonori
2016-09-01
We propose a direct approach for calculating individual energy of polar semiconductor interfaces using density functional theory calculations. This approach is applied to polar interfaces between group-III nitrides (AlN and GaN) and SiC and clarifies the interplay of chemical bonding and charge neutrality at the interface, which is crucial for the stability and polarity of group-III nitrides on SiC substrates. The ideal interface is stabilized among various atomic arrangements over the wide range of the chemical potential on Si-face SiC, whereas those with intermixing are favorable on C-face SiC. The stabilization of the ideal interfaces resulting in Ga-polar GaN and Al-polar AlN films on Si-face SiC is consistent with experiments, suggesting that our approach is versatile to evaluate various polar heterojunction interfaces as well as group-III nitrides on semiconductor substrates.
Human brain mapping: Experimental and computational approaches
Wood, C.C.; George, J.S.; Schmidt, D.M.; Aine, C.J.; Sanders, J.; Belliveau, J.
1998-11-01
This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). This program developed project combined Los Alamos' and collaborators' strengths in noninvasive brain imaging and high performance computing to develop potential contributions to the multi-agency Human Brain Project led by the National Institute of Mental Health. The experimental component of the project emphasized the optimization of spatial and temporal resolution of functional brain imaging by combining: (a) structural MRI measurements of brain anatomy; (b) functional MRI measurements of blood flow and oxygenation; and (c) MEG measurements of time-resolved neuronal population currents. The computational component of the project emphasized development of a high-resolution 3-D volumetric model of the brain based on anatomical MRI, in which structural and functional information from multiple imaging modalities can be integrated into a single computational framework for modeling, visualization, and database representation.
NASA Astrophysics Data System (ADS)
Mehanee, Salah A.
2014-08-01
A very fast and efficient approach for gravity data inversion based on the regularized conjugate gradient method has been developed. This approach simultaneously inverts for the depth ( z), and the amplitude coefficient ( A) of a buried anomalous body from the gravity data measured along a profile. The developed algorithm fits the observed data by a class of some geometrically simple anomalous bodies, including the semi-infinite vertical cylinder, infinitely long horizontal cylinder, and sphere models using the logarithms of the model parameters [log( z) and log(| A|)] rather than the parameters themselves in its iterative minimization scheme. The presented numerical experiments have shown that the original (non-logarithmed) minimization scheme, which uses the parameters themselves ( z and | A|) instead of their logarithms, encountered a variety of convergence problems. The aforementioned transformation of the objective functional subjected to minimization into the space of logarithms of z and | A| overcomes these convergence problems. The reliability and the applicability of the developed algorithm have been demonstrated on several synthetic data sets with and without noise. It is then successfully and carefully applied to seven real data examples with bodies buried in different complex geologic settings and at various depths inside the earth. The method is shown to be highly applicable for mineral exploration, and for both shallow and deep earth imaging, and is of particular value in cases where the observed gravity data is due to an isolated body embedded in the subsurface.
Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.; Browning, Nigel D.
2016-10-17
Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.
Batch Computer Scheduling: A Heuristically Motivated Approach
1974-09-01
Massachusetts, 1957. FRANH 70 Frank, H., I. T. Frisch, and W. Chou, "Topologlcal Considerations In the Design of the ARPA Computor Network," AFIPS...Conference Proceedings, 1970 Spring Joint Computer Conference, pp. 531-587. FRANH 72 FranK, H., R. E. Kahn, and L Kleinrock, " Computor
NASA Astrophysics Data System (ADS)
Ford, Logan; Bajpayee, Abhishek; Techet, Alexandra
2015-11-01
3D particle image velocimetry (PIV) is becoming a popular technique to study biological flows. PIV images that contain fish or other animals around which flow is being studied, need to be appropriately masked in order to remove the animal body from the 3D reconstructed volumes prior to calculating particle displacement vectors. Presented here is a machine learning and synthetic aperture (SA) refocusing based approach for more accurate masking of fish from reconstructed intensity fields for 3D PIV purposes. Using prior knowledge about the 3D shape and appearance of the fish along with SA refocused images at arbitrarily oriented focal planes, the location and orientation of a fish in a reconstructed volume can be accurately determined. Once the location and orientation of a fish in a volume is determined, it can be masked out.
Milman, Mark H
2005-12-01
Astrometric measurements using stellar interferometry rely on precise measurement of the central white light fringe to accurately obtain the optical pathlength difference of incoming starlight to the two arms of the interferometer. One standard approach to stellar interferometry uses a channeled spectrum to determine phases at a number of different wavelengths that are then converted to the pathlength delay. When throughput is low these channels are broadened to improve the signal-to-noise ratio. Ultimately the ability to use monochromatic models and algorithms in each of the channels to extract phase becomes problematic and knowledge of the spectrum must be incorporated to achieve the accuracies required of the astrometric measurements. To accomplish this an optimization problem is posed to estimate simultaneously the pathlength delay and spectrum of the source. Moreover, the nature of the parameterization of the spectrum that is introduced circumvents the need to solve directly for these parameters so that the optimization problem reduces to a scalar problem in just the pathlength delay variable. A number of examples are given to show the robustness of the approach.
Boothroyd, A.I. ); Dove, J.E.; Keogh, W.J. ); Martin, P.G. ); Peterson, M.R. )
1991-09-15
The interaction potential energy surface (PES) of H{sub 4} is of great importance for quantum chemistry, as a test case for molecule--molecule interactions. It is also required for a detailed understanding of certain astrophysical processes, namely, collisional excitation and dissociation of H{sub 2} in molecular clouds, at densities too low to be accessible experimentally. Accurate {ital ab} {ital initio} energies were computed for 6046 conformations of H{sub 4}, using a multiple reference (single and) double excitation configuration interaction (MRD-CI) program. Both systematic and random'' errors were estimated to have an rms size of 0.6 mhartree, for a total rms error of about 0.9 mhartree (or 0.55 kcal/mol) in the final {ital ab} {ital initio} energy values. It proved possible to include in a self-consistent way {ital ab} {ital initio} energies calculated by Schwenke, bringing the number of H{sub 4} conformations to 6101. {ital Ab} {ital initio} energies were also computed for 404 conformations of H{sub 3}; adding {ital ab} {ital initio} energies calculated by other authors yielded a total of 772 conformations of H{sub 3}. (The H{sub 3} results, and an improved analytic PES for H{sub 3}, are reported elsewhere.) {ital Ab} {ital initio} energies are tabulated in this paper only for a sample of H{sub 4} conformations; a full list of all 6101 conformations of H{sub 4} (and 772 conformations of H{sub 3} ) is available from Physics Auxiliary Publication Service (PAPS), or from the authors.
Interpolation Approach To Computer-Generated Holograms
NASA Astrophysics Data System (ADS)
Yatagai, Toyohiko
1983-10-01
A computer-generated hologram (CGH) for reconstructing independent NxN resolution points would actually require a hologram made up of NxN sampling cells. For dependent sampling points of Fourier transform CGHs, the required memory size for computation by using an interpolation technique for reconstructed image points can be reduced. We have made a mosaic hologram which consists of K x K subholograms with N x N sampling points multiplied by an appropriate weighting factor. It is shown that the mosaic hologram can reconstruct an image with NK x NK resolution points. The main advantage of the present algorithm is that a sufficiently large size hologram of NK x NK sample points is synthesized by K x K subholograms which are successively calculated from the data of N x N sample points and also successively plotted.
A Social Construction Approach to Computer Science Education
ERIC Educational Resources Information Center
Machanick, Philip
2007-01-01
Computer science education research has mostly focused on cognitive approaches to learning. Cognitive approaches to understanding learning do not account for all the phenomena observed in teaching and learning. A number of apparently successful educational approaches, such as peer assessment, apprentice-based learning and action learning, have…
A declarative approach to visualizing concurrent computations
Roman, G.C.; Cox, K.C. )
1989-10-01
That visualization can play a key role in the exploration of concurrent computations is central to the ideas presented. Equally important, although given less emphasis, is concern that the full potential of visualization may not be reached unless the art of generating beautiful pictures is rooted in a solid, formally technical foundation. The authors show that program verification provides a formal framework around which such a foundation can be built. Making these ideas a practical reality will require both research and experimentation.
NASA Astrophysics Data System (ADS)
Zhang, Bin; Liang, Chunlei
2015-08-01
This paper presents a simple, efficient, and high-order accurate sliding-mesh interface approach to the spectral difference (SD) method. We demonstrate the approach by solving the two-dimensional compressible Navier-Stokes equations on quadrilateral grids. This approach is an extension of the straight mortar method originally designed for stationary domains [7,8]. Our sliding method creates curved dynamic mortars on sliding-mesh interfaces to couple rotating and stationary domains. On the nonconforming sliding-mesh interfaces, the related variables are first projected from cell faces to mortars to compute common fluxes, and then the common fluxes are projected back from the mortars to the cell faces to ensure conservation. To verify the spatial order of accuracy of the sliding-mesh spectral difference (SSD) method, both inviscid and viscous flow cases are tested. It is shown that the SSD method preserves the high-order accuracy of the SD method. Meanwhile, the SSD method is found to be very efficient in terms of computational cost. This novel sliding-mesh interface method is very suitable for parallel processing with domain decomposition. It can be applied to a wide range of problems, such as the hydrodynamics of marine propellers, the aerodynamics of rotorcraft, wind turbines, and oscillating wing power generators, etc.
Fu, Jian; Tan, Renbo; Chen, Liyuan
2014-01-01
X-ray differential phase-contrast computed tomography (DPC-CT) is a powerful physical and biochemical analysis tool. In practical applications, there are often challenges for DPC-CT due to insufficient data caused by few-view, bad or missing detector channels, or limited scanning angular range. They occur quite frequently because of experimental constraints from imaging hardware, scanning geometry, and the exposure dose delivered to living specimens. In this work, we analyze the influence of incomplete data on DPC-CT image reconstruction. Then, a reconstruction method is developed and investigated for incomplete data DPC-CT. It is based on an algebraic iteration reconstruction technique, which minimizes the image total variation and permits accurate tomographic imaging with less data. This work comprises a numerical study of the method and its experimental verification using a dataset measured at the W2 beamline of the storage ring DORIS III equipped with a Talbot-Lau interferometer. The numerical and experimental results demonstrate that the presented method can handle incomplete data. It will be of interest for a wide range of DPC-CT applications in medicine, biology, and nondestructive testing.
Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data.
Pagán, Josué; De Orbe, M Irene; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L; Mora, J Vivancos; Moya, José M; Ayala, José L
2015-06-30
Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives.
Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data
Pagán, Josué; Irene De Orbe, M.; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L.; Vivancos Mora, J.; Moya, José M.; Ayala, José L.
2015-01-01
Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives. PMID:26134103
NASA Technical Reports Server (NTRS)
Lindner, Bernhard Lee; Ackerman, Thomas P.; Pollack, James B.
1990-01-01
CO2 comprises 95 pct. of the composition of the Martian atmosphere. However, the Martian atmosphere also has a high aerosol content. Dust particles vary from less than 0.2 to greater than 3.0. CO2 is an active absorber and emitter in near IR and IR wavelengths; the near IR absorption bands of CO2 provide significant heating of the atmosphere, and the 15 micron band provides rapid cooling. Including both CO2 and aerosol radiative transfer simultaneously in a model is difficult. Aerosol radiative transfer requires a multiple scattering code, while CO2 radiative transfer must deal with complex wavelength structure. As an alternative to the pure atmosphere treatment in most models which causes inaccuracies, a treatment was developed called the exponential sum or k distribution approximation. The chief advantage of the exponential sum approach is that the integration over k space of f(k) can be computed more quickly than the integration of k sub upsilon over frequency. The exponential sum approach is superior to the photon path distribution and emissivity techniques for dusty conditions. This study was the first application of the exponential sum approach to Martian conditions.
Kong, Hao; Ma, Zhuoran; Wang, Song; Gong, Xiaoyun; Zhang, Sichun; Zhang, Xinrong
2014-08-05
With the inspiration of an ancient Chinese poison test approach, we report a rapid hydrogen sulfide detection strategy in specific areas of live cells using silver needles with good spatial resolution of 2 × 2 μm(2). Besides the accurate-localization ability, this reflection-based strategy also has attractive merits of convenience and robust response when free pretreatment and short detection time are concerned. The success of endogenous H2S level evaluation in cellular cytoplasm and nuclear of human A549 cells promises the application potential of our strategy in scientific research and medical diagnosis.
Computational Approaches to Simulation and Optimization of Global Aircraft Trajectories
NASA Technical Reports Server (NTRS)
Ng, Hok Kwan; Sridhar, Banavar
2016-01-01
This study examines three possible approaches to improving the speed in generating wind-optimal routes for air traffic at the national or global level. They are: (a) using the resources of a supercomputer, (b) running the computations on multiple commercially available computers and (c) implementing those same algorithms into NASAs Future ATM Concepts Evaluation Tool (FACET) and compares those to a standard implementation run on a single CPU. Wind-optimal aircraft trajectories are computed using global air traffic schedules. The run time and wait time on the supercomputer for trajectory optimization using various numbers of CPUs ranging from 80 to 10,240 units are compared with the total computational time for running the same computation on a single desktop computer and on multiple commercially available computers for potential computational enhancement through parallel processing on the computer clusters. This study also re-implements the trajectory optimization algorithm for further reduction of computational time through algorithm modifications and integrates that with FACET to facilitate the use of the new features which calculate time-optimal routes between worldwide airport pairs in a wind field for use with existing FACET applications. The implementations of trajectory optimization algorithms use MATLAB, Python, and Java programming languages. The performance evaluations are done by comparing their computational efficiencies and based on the potential application of optimized trajectories. The paper shows that in the absence of special privileges on a supercomputer, a cluster of commercially available computers provides a feasible approach for national and global air traffic system studies.
Information theoretic approaches to multidimensional neural computations
NASA Astrophysics Data System (ADS)
Fitzgerald, Jeffrey D.
Many systems in nature process information by transforming inputs from their environments into observable output states. These systems are often difficult to study because they are performing computations on multidimensional inputs with many degrees of freedom using highly nonlinear functions. The work presented in this dissertation deals with some of the issues involved with characterizing real-world input/output systems and understanding the properties of idealized systems using information theoretic methods. Using the principle of maximum entropy, a family of models are created that are consistent with certain measurable correlations from an input/output dataset but are maximally unbiased in all other respects, thereby eliminating all unjustified assumptions about the computation. In certain cases, including spiking neurons, we show that these models also minimize the mutual information. This property gives one the advantage of being able to identify the relevant input/output statistics by calculating their information content. We argue that these maximum entropy models provide a much needed quantitative framework for characterizing and understanding sensory processing neurons that are selective for multiple stimulus features. To demonstrate their usefulness, these ideas are applied to neural recordings from macaque retina and thalamus. These neurons, which primarily respond to two stimulus features, are shown to be well described using only first and second order statistics, indicating that their firing rates encode information about stimulus correlations. In addition to modeling multi-feature computations in the relevant feature space, we also show that maximum entropy models are capable of discovering the relevant feature space themselves. This technique overcomes the disadvantages of two commonly used dimensionality reduction methods and is explored using several simulated neurons, as well as retinal and thalamic recordings. Finally, we ask how neurons in a
A Computational Approach to Competitive Range Expansions
NASA Astrophysics Data System (ADS)
Weber, Markus F.; Poxleitner, Gabriele; Hebisch, Elke; Frey, Erwin; Opitz, Madeleine
2014-03-01
Bacterial communities represent complex and dynamic ecological systems. Environmental conditions and microbial interactions determine whether a bacterial strain survives an expansion to new territory. In our work, we studied competitive range expansions in a model system of three Escherichia coli strains. In this system, a colicin producing strain competed with a colicin resistant, and with a colicin sensitive strain for new territory. Genetic engineering allowed us to tune the strains' growth rates and to study their expansion in distinct ecological scenarios (with either cyclic or hierarchical dominance). The control over growth rates also enabled us to construct and to validate a predictive computational model of the bacterial dynamics. The model rested on an agent-based, coarse-grained description of the expansion process and we conducted independent experiments on the growth of single-strain colonies for its parametrization. Furthermore, the model considered the long-range nature of the toxin interaction between strains. The integration of experimental analysis with computational modeling made it possible to quantify how the level of biodiversity depends on the interplay between bacterial growth rates, the initial composition of the inoculum, and the toxin range.
Novel Computational Approaches to Drug Discovery
NASA Astrophysics Data System (ADS)
Skolnick, Jeffrey; Brylinski, Michal
2010-01-01
New approaches to protein functional inference based on protein structure and evolution are described. First, FINDSITE, a threading based approach to protein function prediction, is summarized. Then, the results of large scale benchmarking of ligand binding site prediction, ligand screening, including applications to HIV protease, and GO molecular functional inference are presented. A key advantage of FINDSITE is its ability to use low resolution, predicted structures as well as high resolution experimental structures. Then, an extension of FINDSITE to ligand screening in GPCRs using predicted GPCR structures, FINDSITE/QDOCKX, is presented. This is a particularly difficult case as there are few experimentally solved GPCR structures. Thus, we first train on a subset of known binding ligands for a set of GPCRs; this is then followed by benchmarking against a large ligand library. For the virtual ligand screening of a number of Dopamine receptors, encouraging results are seen, with significant enrichment in identified ligands over those found in the training set. Thus, FINDSITE and its extensions represent a powerful approach to the successful prediction of a variety of molecular functions.
Computational approaches to natural product discovery
Medema, Marnix H.; Fischbach, Michael A.
2016-01-01
From the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data, and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering long-standing questions in microbial ecology regarding the roles of metabolites in interspecies interactions. PMID:26284671
Computational approaches to natural product discovery.
Medema, Marnix H; Fischbach, Michael A
2015-09-01
Starting with the earliest Streptomyces genome sequences, the promise of natural product genome mining has been captivating: genomics and bioinformatics would transform compound discovery from an ad hoc pursuit to a high-throughput endeavor. Until recently, however, genome mining has advanced natural product discovery only modestly. Here, we argue that the development of algorithms to mine the continuously increasing amounts of (meta)genomic data will enable the promise of genome mining to be realized. We review computational strategies that have been developed to identify biosynthetic gene clusters in genome sequences and predict the chemical structures of their products. We then discuss networking strategies that can systematize large volumes of genetic and chemical data and connect genomic information to metabolomic and phenotypic data. Finally, we provide a vision of what natural product discovery might look like in the future, specifically considering longstanding questions in microbial ecology regarding the roles of metabolites in interspecies interactions.
Numerical Computation of Sensitivities and the Adjoint Approach
NASA Technical Reports Server (NTRS)
Lewis, Robert Michael
1997-01-01
We discuss the numerical computation of sensitivities via the adjoint approach in optimization problems governed by differential equations. We focus on the adjoint problem in its weak form. We show how one can avoid some of the problems with the adjoint approach, such as deriving suitable boundary conditions for the adjoint equation. We discuss the convergence of numerical approximations of the costate computed via the weak form of the adjoint problem and show the significance for the discrete adjoint problem.
A Social Constructivist Approach to Computer-Mediated Instruction.
ERIC Educational Resources Information Center
Pear, Joseph J.; Crone-Todd, Darlene E.
2002-01-01
Describes a computer-mediated teaching system called computer-aided personalized system of instruction (CAPSI) that incorporates a social constructivist approach, maintaining that learning occurs primarily through a socially interactive process. Discusses use of CAPSI in an undergraduate course at the University of Manitoba that showed students…
Computational Approaches for Understanding Energy Metabolism
Shestov, Alexander A; Barker, Brandon; Gu, Zhenglong; Locasale, Jason W
2013-01-01
There has been a surge of interest in understanding the regulation of metabolic networks involved in disease in recent years. Quantitative models are increasingly being used to i nterrogate the metabolic pathways that are contained within this complex disease biology. At the core of this effort is the mathematical modeling of central carbon metabolism involving glycolysis and the citric acid cycle (referred to as energy metabolism). Here we discuss several approaches used to quantitatively model metabolic pathways relating to energy metabolism and discuss their formalisms, successes, and limitations. PMID:23897661
Yildiz, Dilan; Bozkaya, Uğur
2016-01-30
The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials and electron affinities from any level of theory. Although it is widely applied to ionization potentials, the EKT approach has not been applied to evaluation of the chemical reactivity. We present the first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω). We assess the performance of the EKT approaches for post-Hartree-Fock methods, such as Møller-Plesset perturbation theory, the coupled-electron pair theory, and their orbital-optimized counterparts for the evaluation of the chemical reactivity. Especially, results of the orbital-optimized coupled-electron pair theory method (with the aug-cc-pVQZ basis set) for predictions of the chemical reactivity are very promising; the corresponding mean absolute errors are 0.16, 0.28, and 0.09 eV for μ, η, and ω, respectively.
In silico drug discovery approaches on grid computing infrastructures.
Wolf, Antje; Shahid, Mohammad; Kasam, Vinod; Ziegler, Wolfgang; Hofmann-Apitius, Martin
2010-02-01
The first step in finding a "drug" is screening chemical compound databases against a protein target. In silico approaches like virtual screening by molecular docking are well established in modern drug discovery. As molecular databases of compounds and target structures are becoming larger and more and more computational screening approaches are available, there is an increased need in compute power and more complex workflows. In this regard, computational Grids are predestined and offer seamless compute and storage capacity. In recent projects related to pharmaceutical research, the high computational and data storage demands of large-scale in silico drug discovery approaches have been addressed by using Grid computing infrastructures, in both; pharmaceutical industry as well as academic research. Grid infrastructures are part of the so-called eScience paradigm, where a digital infrastructure supports collaborative processes by providing relevant resources and tools for data- and compute-intensive applications. Substantial computing resources, large data collections and services for data analysis are shared on the Grid infrastructure and can be mobilized on demand. This review gives an overview on the use of Grid computing for in silico drug discovery and tries to provide a vision of future development of more complex and integrated workflows on Grids, spanning from target identification and target validation via protein-structure and ligand dependent screenings to advanced mining of large scale in silico experiments.
An integrated experimental and computational approach for ...
Enantiomers of chiral molecules commonly exhibit differing pharmacokinetics and toxicities, which can introduce significant uncertainty when evaluating biological and environmental fates and potential risks to humans and the environment. However, racemization (the irreversible transformation of one enantiomer into the racemic mixture) and enantiomerization (the reversible conversion of one enantiomer into the other) are poorly understood. To better understand these processes, we investigated the chiral fungicide, triadimefon, which undergoes racemization in soils, water, and organic solvents. Nuclear magnetic resonance (NMR) and gas chromatography / mass spectrometry (GC/MS) techniques were used to measure the rates of enantiomerization and racemization, deuterium isotope effects, and activation energies for triadimefon in H2O and D2O. From these results we were able to determine that: 1) the alpha-carbonyl carbon of triadimefon is the reaction site; 2) cleavage of the C-H (C-D) bond is the rate-determining step; 3) the reaction is base-catalyzed; and 4) the reaction likely involves a symmetrical intermediate. The B3LYP/6–311 + G** level of theory was used to compute optimized geometries, harmonic vibrational frequencies, nature population analysis, and intrinsic reaction coordinates for triadimefon in water and three racemization pathways were hypothesized. This work provides an initial step in developing predictive, structure-based models that are needed to
NASA Astrophysics Data System (ADS)
Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel
The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.
Multivariate analysis: A statistical approach for computations
NASA Astrophysics Data System (ADS)
Michu, Sachin; Kaushik, Vandana
2014-10-01
Multivariate analysis is a type of multivariate statistical approach commonly used in, automotive diagnosis, education evaluating clusters in finance etc and more recently in the health-related professions. The objective of the paper is to provide a detailed exploratory discussion about factor analysis (FA) in image retrieval method and correlation analysis (CA) of network traffic. Image retrieval methods aim to retrieve relevant images from a collected database, based on their content. The problem is made more difficult due to the high dimension of the variable space in which the images are represented. Multivariate correlation analysis proposes an anomaly detection and analysis method based on the correlation coefficient matrix. Anomaly behaviors in the network include the various attacks on the network like DDOs attacks and network scanning.
Brahme, Anders; Nyman, Peter; Skatt, Björn
2008-05-01
A four-dimensional (4D) laser camera (LC) has been developed for accurate patient imaging in diagnostic and therapeutic radiology. A complementary metal-oxide semiconductor camera images the intersection of a scanned fan shaped laser beam with the surface of the patient and allows real time recording of movements in a three-dimensional (3D) or four-dimensional (4D) format (3D +time). The LC system was first designed as an accurate patient setup tool during diagnostic and therapeutic applications but was found to be of much wider applicability as a general 4D photon "tag" for the surface of the patient in different clinical procedures. It is presently used as a 3D or 4D optical benchmark or tag for accurate delineation of the patient surface as demonstrated for patient auto setup, breathing and heart motion detection. Furthermore, its future potential applications in gating, adaptive therapy, 3D or 4D image fusion between most imaging modalities and image processing are discussed. It is shown that the LC system has a geometrical resolution of about 0, 1 mm and that the rigid body repositioning accuracy is about 0, 5 mm below 20 mm displacements, 1 mm below 40 mm and better than 2 mm at 70 mm. This indicates a slight need for repeated repositioning when the initial error is larger than about 50 mm. The positioning accuracy with standard patient setup procedures for prostate cancer at Karolinska was found to be about 5-6 mm when independently measured using the LC system. The system was found valuable for positron emission tomography-computed tomography (PET-CT) in vivo tumor and dose delivery imaging where it potentially may allow effective correction for breathing artifacts in 4D PET-CT and image fusion with lymph node atlases for accurate target volume definition in oncology. With a LC system in all imaging and radiation therapy rooms, auto setup during repeated diagnostic and therapeutic procedures may save around 5 min per session, increase accuracy and allow
Mutations that Cause Human Disease: A Computational/Experimental Approach
Beernink, P; Barsky, D; Pesavento, B
2006-01-11
International genome sequencing projects have produced billions of nucleotides (letters) of DNA sequence data, including the complete genome sequences of 74 organisms. These genome sequences have created many new scientific opportunities, including the ability to identify sequence variations among individuals within a species. These genetic differences, which are known as single nucleotide polymorphisms (SNPs), are particularly important in understanding the genetic basis for disease susceptibility. Since the report of the complete human genome sequence, over two million human SNPs have been identified, including a large-scale comparison of an entire chromosome from twenty individuals. Of the protein coding SNPs (cSNPs), approximately half leads to a single amino acid change in the encoded protein (non-synonymous coding SNPs). Most of these changes are functionally silent, while the remainder negatively impact the protein and sometimes cause human disease. To date, over 550 SNPs have been found to cause single locus (monogenic) diseases and many others have been associated with polygenic diseases. SNPs have been linked to specific human diseases, including late-onset Parkinson disease, autism, rheumatoid arthritis and cancer. The ability to predict accurately the effects of these SNPs on protein function would represent a major advance toward understanding these diseases. To date several attempts have been made toward predicting the effects of such mutations. The most successful of these is a computational approach called ''Sorting Intolerant From Tolerant'' (SIFT). This method uses sequence conservation among many similar proteins to predict which residues in a protein are functionally important. However, this method suffers from several limitations. First, a query sequence must have a sufficient number of relatives to infer sequence conservation. Second, this method does not make use of or provide any information on protein structure, which can be used to
Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi; Rossi, Simone
2015-11-12
Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear and nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.
Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi; ...
2015-11-12
Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear andmore » nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.« less
NASA Astrophysics Data System (ADS)
Gan, Chenquan; Yang, Xiaofan; Liu, Wanping; Zhu, Qingyi; Jin, Jian; He, Li
2014-08-01
Based on the assumption that external computers (particularly, infected external computers) are connected to the Internet, and by considering the influence of the Internet topology on computer virus spreading, this paper establishes a novel computer virus propagation model with a complex-network approach. This model possesses a unique (viral) equilibrium which is globally attractive. Some numerical simulations are also given to illustrate this result. Further study shows that the computers with higher node degrees are more susceptible to infection than those with lower node degrees. In this regard, some appropriate protective measures are suggested.
NASA Astrophysics Data System (ADS)
Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S.; Shirley, Eric L.; Prendergast, David
2017-03-01
Constrained-occupancy delta-self-consistent-field (Δ SCF ) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1 s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The Δ SCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle Δ SCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.
Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M
2012-07-01
We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking.
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-09-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups, and then it constructs the Voronoi diagram between the two groups using the triangular network. After this, the normal of each Voronoi edge is calculated, and the quantitative expression of the direction relations is constructed. Finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
An approach to computing direction relations between separated object groups
NASA Astrophysics Data System (ADS)
Yan, H.; Wang, Z.; Li, J.
2013-06-01
Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on Gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups; and then it constructs the Voronoi Diagram between the two groups using the triangular network; after this, the normal of each Vornoi edge is calculated, and the quantitative expression of the direction relations is constructed; finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.
A tale of three bio-inspired computational approaches
NASA Astrophysics Data System (ADS)
Schaffer, J. David
2014-05-01
I will provide a high level walk-through for three computational approaches derived from Nature. First, evolutionary computation implements what we may call the "mother of all adaptive processes." Some variants on the basic algorithms will be sketched and some lessons I have gleaned from three decades of working with EC will be covered. Then neural networks, computational approaches that have long been studied as possible ways to make "thinking machines", an old dream of man's, and based upon the only known existing example of intelligence. Then, a little overview of attempts to combine these two approaches that some hope will allow us to evolve machines we could never hand-craft. Finally, I will touch on artificial immune systems, Nature's highly sophisticated defense mechanism, that has emerged in two major stages, the innate and the adaptive immune systems. This technology is finding applications in the cyber security world.
Sensing and perception: Connectionist approaches to subcognitive computing
NASA Technical Reports Server (NTRS)
Skrrypek, J.
1987-01-01
New approaches to machine sensing and perception are presented. The motivation for crossdisciplinary studies of perception in terms of AI and neurosciences is suggested. The question of computing architecture granularity as related to global/local computation underlying perceptual function is considered and examples of two environments are given. Finally, the examples of using one of the environments, UCLA PUNNS, to study neural architectures for visual function are presented.
The process group approach to reliable distributed computing
NASA Technical Reports Server (NTRS)
Birman, Kenneth P.
1992-01-01
The difficulty of developing reliable distribution software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems that are substantially easier to develop, exploit sophisticated forms of cooperative computation, and achieve high reliability. Six years of research on ISIS, describing the model, its implementation challenges, and the types of applications to which ISIS has been applied are reviewed.
Buytaert, Jan A N; Salih, Wasil H M; Dierick, Manual; Jacobs, Patric; Dirckx, Joris J J
2011-12-01
In order to improve realism in middle ear (ME) finite-element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain these data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution μCT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art μCT delivers high-resolution data on the 3D shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting 3D model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model, and discuss the morphological properties of the soft tissue structures, such as muscles and ligaments.
NASA Astrophysics Data System (ADS)
Huang, X.; Schwenke, D.; Lee, T. J.
2014-12-01
Last year we reported a semi-empirical 32S16O2 spectroscopic line list (denoted Ames-296K) for its atmospheric characterization in Venus and other Exoplanetary environments. In order to facilitate the Sulfur isotopic ratio and Sulfur chemistry model determination, now we present Ames-296K line lists for both 626 (upgraded) and other 4 symmetric isotopologues: 636, 646, 666 and 828. The line lists are computed on an ab initio potential energy surface refined with most reliable high resolution experimental data, using a high quality CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface. The most valuable part of our approach is to provide "truly reliable" predictions (and alternatives) for those unknown or hard-to-measure/analyze spectra. This strategy has guaranteed the lists are the best available alternative for those wide spectra region missing from spectroscopic databases such as HITRAN and GEISA, where only very limited data exist for 626/646 and no Infrared data at all for 636/666 or other minor isotopologues. Our general line position accuracy up to 5000 cm-1 is 0.01 - 0.02 cm-1 or better. Most transition intensity deviations are less than 5%, compare to experimentally measured quantities. Note that we have solved a convergence issue and further improved the quality and completeness of the main isotopologue 626 list at 296K. We will compare the lists to available models in CDMS/JPL/HITRAN and discuss the future mutually beneficial interactions between theoretical and experimental efforts.
A distributed computing approach to mission operations support. [for spacecraft
NASA Technical Reports Server (NTRS)
Larsen, R. L.
1975-01-01
Computing mission operation support includes orbit determination, attitude processing, maneuver computation, resource scheduling, etc. The large-scale third-generation distributed computer network discussed is capable of fulfilling these dynamic requirements. It is shown that distribution of resources and control leads to increased reliability, and exhibits potential for incremental growth. Through functional specialization, a distributed system may be tuned to very specific operational requirements. Fundamental to the approach is the notion of process-to-process communication, which is effected through a high-bandwidth communications network. Both resource-sharing and load-sharing may be realized in the system.
Wang, Zhiheng; Yang, Qianqian; Li, Tonghua; Cong, Peisheng
2015-01-01
The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS) obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database. Availability The DisoMCS is available at http://cal.tongji.edu.cn/disorder/. PMID:26090958
Singh, Nidhi; Warshel, Arieh
2009-01-01
effectively captures the physics of these entropic effects. The success of the current approach indicates that it should be applicable to the studies of the solvation entropies in the proteins and also, in examining hydrophobic effects. Thus, we believe that the RR approach provides a powerful tool for evaluating the corresponding contributions to the binding entropies and eventually, to the binding free energies. This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design. PMID:19402609
Oyedepo, Gbenga A; Wilson, Angela K
2010-08-26
The correlation consistent Composite Approach, ccCA [ Deyonker , N. J. ; Cundari , T. R. ; Wilson , A. K. J. Chem. Phys. 2006 , 124 , 114104 ] has been demonstrated to predict accurate thermochemical properties of chemical species that can be described by a single configurational reference state, and at reduced computational cost, as compared with ab initio methods such as CCSD(T) used in combination with large basis sets. We have developed three variants of a multireference equivalent of this successful theoretical model. The method, called the multireference correlation consistent composite approach (MR-ccCA), is designed to predict the thermochemical properties of reactive intermediates, excited state species, and transition states to within chemical accuracy (e.g., 1 kcal/mol for enthalpies of formation) of reliable experimental values. In this study, we have demonstrated the utility of MR-ccCA: (1) in the determination of the adiabatic singlet-triplet energy separations and enthalpies of formation for the ground states for a set of diradicals and unsaturated compounds, and (2) in the prediction of energetic barriers to internal rotation, in ethylene and its heavier congener, disilene. Additionally, we have utilized MR-ccCA to predict the enthalpies of formation of the low-lying excited states of all the species considered. MR-ccCA is shown to give quantitative results without reliance upon empirically derived parameters, making it suitable for application to study novel chemical systems with significant nondynamical correlation effects.
Novel Approaches to Quantum Computation Using Solid State Qubits
2007-12-31
Han, A scheme for the teleportation of multiqubit quantum information via the control of many agents in a network, submitted to Phys. Lett. A, 343...approach, Phys. Rev. B 70, 094513 (2004). 22. C.-P. Yang, S.-I. Chu, and S. Han, Efficient many party controlled teleportation of multiqubit quantum ...June 1, 2001- September 30, 2007 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER "Novel Approaches to Quantum Computation Using Solid State Qubits" F49620
General Approach in Computing Sums of Products of Binary Sequences
2011-12-08
General Approach in Computing Sums of Products of Binary Sequences E. Kiliç1, P. Stănică2 1TOBB Economics and Technology University, Mathematics...pstanica@nps.edu December 8, 2011 Abstract In this paper we find a general approach to find closed forms of sums of products of arbitrary sequences ...satisfying the same recurrence with different initial conditions. We apply successfully our technique to sums of products of such sequences with indices in
NASA Astrophysics Data System (ADS)
Martin, Y. L.
The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species
Computational approach to the study of thermal spin crossover phenomena
Rudavskyi, Andrii; Broer, Ria; Sousa, Carmen
2014-05-14
The key parameters associated to the thermally induced spin crossover process have been calculated for a series of Fe(II) complexes with mono-, bi-, and tridentate ligands. Combination of density functional theory calculations for the geometries and for normal vibrational modes, and highly correlated wave function methods for the energies, allows us to accurately compute the entropy variation associated to the spin transition and the zero-point corrected energy difference between the low- and high-spin states. From these values, the transition temperature, T{sub 1/2}, is estimated for different compounds.
New Theoretical Approaches for Human-Computer Interaction.
ERIC Educational Resources Information Center
Rogers, Yvonne
2004-01-01
Presents a critique of recent theoretical developments in the field of human-computer interaction (HCI) together with an overview of HCI practice. This chapter discusses why theoretically based approaches have had little impact on the practice of interaction design and suggests mechanisms to enable designers and researchers to better articulate…
Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won
2010-01-01
Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE-MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn; 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. By combining these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. PMID:20863060
Computing solvent-induced forces in the solvation approach called Semi Explicit Assembly
NASA Astrophysics Data System (ADS)
Brini, Emiliano; Hummel, Michelle H.; Coutsias, Evangelos A.; Fennell, Christopher J.; Dill, Ken A.
2014-03-01
Many biologically relevant processes (e.g. protein folding) are often too big and slow to be simulated by computer methods that model atomically detailed water. Faster physical models of water are needed. We have developed an approach called Semi Explicit Assembly (SEA) [C.J. Fennell, C.W. Kehoe, K.A. Dill, PNAS, 108, 3234 (2011)]. It is physical because it uses pre-simulations of explicit-solvent models, and it is fast because at runtime, we just combine the pre-simulated results in rapid computations. SEA has also now been proven physically accurate in two blind tests called SAMPL. Here, we describe the computation of solvation forces in SEA, so that this solvation procedure can be incorporated into standard molecular dynamics codes. We describe experimental tests.
Time-Accurate, Unstructured-Mesh Navier-Stokes Computations with the Space-Time CESE Method
NASA Technical Reports Server (NTRS)
Chang, Chau-Lyan
2006-01-01
Application of the newly emerged space-time conservation element solution element (CESE) method to compressible Navier-Stokes equations is studied. In contrast to Euler equations solvers, several issues such as boundary conditions, numerical dissipation, and grid stiffness warrant systematic investigations and validations. Non-reflecting boundary conditions applied at the truncated boundary are also investigated from the stand point of acoustic wave propagation. Validations of the numerical solutions are performed by comparing with exact solutions for steady-state as well as time-accurate viscous flow problems. The test cases cover a broad speed regime for problems ranging from acoustic wave propagation to 3D hypersonic configurations. Model problems pertinent to hypersonic configurations demonstrate the effectiveness of the CESE method in treating flows with shocks, unsteady waves, and separations. Good agreement with exact solutions suggests that the space-time CESE method provides a viable alternative for time-accurate Navier-Stokes calculations of a broad range of problems.
Sengupta, Arkajyoti; Ramabhadran, Raghunath O; Raghavachari, Krishnan
2014-08-14
In this study we have used the connectivity-based hierarchy (CBH) method to derive accurate heats of formation of a range of biomolecules, 18 amino acids and 10 barbituric acid/uracil derivatives. The hierarchy is based on the connectivity of the different atoms in a large molecule. It results in error-cancellation reaction schemes that are automated, general, and can be readily used for a broad range of organic molecules and biomolecules. Herein, we first locate stable conformational and tautomeric forms of these biomolecules using an accurate level of theory (viz. CCSD(T)/6-311++G(3df,2p)). Subsequently, the heats of formation of the amino acids are evaluated using the CBH-1 and CBH-2 schemes and routinely employed density functionals or wave function-based methods. The calculated heats of formation obtained herein using modest levels of theory and are in very good agreement with those obtained using more expensive W1-F12 and W2-F12 methods on amino acids and G3 results on barbituric acid derivatives. Overall, the present study (a) highlights the small effect of including multiple conformers in determining the heats of formation of biomolecules and (b) in concurrence with previous CBH studies, proves that use of the more effective error-cancelling isoatomic scheme (CBH-2) results in more accurate heats of formation with modestly sized basis sets along with common density functionals or wave function-based methods.
Computational intelligence approaches for pattern discovery in biological systems.
Fogel, Gary B
2008-07-01
Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.
NASA Astrophysics Data System (ADS)
Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.
2009-12-01
FILMPAR is a highly efficient and portable parallel multigrid algorithm for solving a discretised form of the lubrication approximation to three-dimensional, gravity-driven, continuous thin film free-surface flow over substrates containing micro-scale topography. While generally applicable to problems involving heterogeneous and distributed features, for illustrative purposes the algorithm is benchmarked on a distributed memory IBM BlueGene/P computing platform for the case of flow over a single trench topography, enabling direct comparison with complementary experimental data and existing serial multigrid solutions. Parallel performance is assessed as a function of the number of processors employed and shown to lead to super-linear behaviour for the production of mesh-independent solutions. In addition, the approach is used to solve for the case of flow over a complex inter-connected topographical feature and a description provided of how FILMPAR could be adapted relatively simply to solve for a wider class of related thin film flow problems. Program summaryProgram title: FILMPAR Catalogue identifier: AEEL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 530 421 No. of bytes in distributed program, including test data, etc.: 1 960 313 Distribution format: tar.gz Programming language: C++ and MPI Computer: Desktop, server Operating system: Unix/Linux Mac OS X Has the code been vectorised or parallelised?: Yes. Tested with up to 128 processors RAM: 512 MBytes Classification: 12 External routines: GNU C/C++, MPI Nature of problem: Thin film flows over functional substrates containing well-defined single and complex topographical features are of enormous significance, having a wide variety of engineering
Cloud computing approaches to accelerate drug discovery value chain.
Garg, Vibhav; Arora, Suchir; Gupta, Chitra
2011-12-01
Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.
NASA Astrophysics Data System (ADS)
Ahnen, Sandra; Hehn, Anna-Sophia; Vogiatzis, Konstantinos D.; Trachsel, Maria A.; Leutwyler, Samuel; Klopper, Wim
2014-09-01
Using explicitly-correlated coupled-cluster theory with single and double excitations, the intermolecular distances and interaction energies of the T-shaped imidazole⋯benzene and pyrrole⋯benzene complexes have been computed in a large augmented correlation-consistent quadruple-zeta basis set, adding also corrections for connected triple excitations and remaining basis-set-superposition errors. The results of these computations are used to assess other methods such as Møller-Plesset perturbation theory (MP2), spin-component-scaled MP2 theory, dispersion-weighted MP2 theory, interference-corrected explicitly-correlated MP2 theory, dispersion-corrected double-hybrid density-functional theory (DFT), DFT-based symmetry-adapted perturbation theory, the random-phase approximation, explicitly-correlated ring-coupled-cluster-doubles theory, and double-hybrid DFT with a correlation energy computed in the random-phase approximation.
NASA Astrophysics Data System (ADS)
Shi, Guangyuan; Li, Song; Huang, Ke; Li, Zile; Zheng, Guoxing
2016-10-01
We have developed a new numerical ray-tracing approach for LIDAR signal power function computation, in which the light round-trip propagation is analyzed by geometrical optics and a simple experiment is employed to acquire the laser intensity distribution. It is relatively more accurate and flexible than previous methods. We emphatically discuss the relationship between the inclined angle and the dynamic range of detector output signal in biaxial LIDAR system. Results indicate that an appropriate negative angle can compress the signal dynamic range. This technique has been successfully proved by comparison with real measurements.
Computing 3-D steady supersonic flow via a new Lagrangian approach
NASA Technical Reports Server (NTRS)
Loh, C. Y.; Liou, M.-S.
1993-01-01
The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.
Analytical and Computational Properties of Distributed Approaches to MDO
NASA Technical Reports Server (NTRS)
Alexandrov, Natalia M.; Lewis, Robert Michael
2000-01-01
Historical evolution of engineering disciplines and the complexity of the MDO problem suggest that disciplinary autonomy is a desirable goal in formulating and solving MDO problems. We examine the notion of disciplinary autonomy and discuss the analytical properties of three approaches to formulating and solving MDO problems that achieve varying degrees of autonomy by distributing the problem along disciplinary lines. Two of the approaches-Optimization by Linear Decomposition and Collaborative Optimization-are based on bi-level optimization and reflect what we call a structural perspective. The third approach, Distributed Analysis Optimization, is a single-level approach that arises from what we call an algorithmic perspective. The main conclusion of the paper is that disciplinary autonomy may come at a price: in the bi-level approaches, the system-level constraints introduced to relax the interdisciplinary coupling and enable disciplinary autonomy can cause analytical and computational difficulties for optimization algorithms. The single-level alternative we discuss affords a more limited degree of autonomy than that of the bi-level approaches, but without the computational difficulties of the bi-level methods. Key Words: Autonomy, bi-level optimization, distributed optimization, multidisciplinary optimization, multilevel optimization, nonlinear programming, problem integration, system synthesis
One approach for evaluating the Distributed Computing Design System (DCDS)
NASA Technical Reports Server (NTRS)
Ellis, J. T.
1985-01-01
The Distributed Computer Design System (DCDS) provides an integrated environment to support the life cycle of developing real-time distributed computing systems. The primary focus of DCDS is to significantly increase system reliability and software development productivity, and to minimize schedule and cost risk. DCDS consists of integrated methodologies, languages, and tools to support the life cycle of developing distributed software and systems. Smooth and well-defined transistions from phase to phase, language to language, and tool to tool provide a unique and unified environment. An approach to evaluating DCDS highlights its benefits.
The DYNAMO Simulation Language--An Alternate Approach to Computer Science Education.
ERIC Educational Resources Information Center
Bronson, Richard
1986-01-01
Suggests the use of computer simulation of continuous systems as a problem solving approach to computer languages. Outlines the procedures that the system dynamics approach employs in computer simulations. Explains the advantages of the special purpose language, DYNAMO. (ML)
Protein Engineering by Combined Computational and In Vitro Evolution Approaches.
Rosenfeld, Lior; Heyne, Michael; Shifman, Julia M; Papo, Niv
2016-05-01
Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.
A computer-aided approach to nonlinear control systhesis
NASA Technical Reports Server (NTRS)
Wie, Bong; Anthony, Tobin
1988-01-01
The major objective of this project is to develop a computer-aided approach to nonlinear stability analysis and nonlinear control system design. This goal is to be obtained by refining the describing function method as a synthesis tool for nonlinear control design. The interim report outlines the approach by this study to meet these goals including an introduction to the INteractive Controls Analysis (INCA) program which was instrumental in meeting these study objectives. A single-input describing function (SIDF) design methodology was developed in this study; coupled with the software constructed in this study, the results of this project provide a comprehensive tool for design and integration of nonlinear control systems.
Style: A Computational and Conceptual Blending-Based Approach
NASA Astrophysics Data System (ADS)
Goguen, Joseph A.; Harrell, D. Fox
This chapter proposes a new approach to style, arising from our work on computational media using structural blending, which enriches the conceptual blending of cognitive linguistics with structure building operations in order to encompass syntax and narrative as well as metaphor. We have implemented both conceptual and structural blending, and conducted initial experiments with poetry, including interactive multimedia poetry, although the approach generalizes to other media. The central idea is to generate multimedia content and analyze style in terms of blending principles, based on our finding that different principles from those of common sense blending are often needed for some contemporary poetic metaphors.
The Visualization Management System Approach To Visualization In Scientific Computing
NASA Astrophysics Data System (ADS)
Butler, David M.; Pendley, Michael H.
1989-09-01
We introduce the visualization management system (ViMS), a new approach to the development of software for visualization in scientific computing (ViSC). The conceptual foundation for a ViMS is an abstract visualization model which specifies a class of geometric objects, the graphic representations of the objects and the operations on both. A ViMS provides a modular implementation of its visualization model. We describe ViMS requirements and a model-independent ViMS architecture. We briefly describe the vector bundle visualization model and the visualization taxonomy it generates. We conclude by summarizing the benefits of the ViMS approach.
Beyond the Melnikov method: A computer assisted approach
NASA Astrophysics Data System (ADS)
Capiński, Maciej J.; Zgliczyński, Piotr
2017-01-01
We present a Melnikov type approach for establishing transversal intersections of stable/unstable manifolds of perturbed normally hyperbolic invariant manifolds (NHIMs). The method is based on a new geometric proof of the normally hyperbolic invariant manifold theorem, which establishes the existence of a NHIM, together with its associated invariant manifolds and bounds on their first and second derivatives. We do not need to know the explicit formulas for the homoclinic orbits prior to the perturbation. We also do not need to compute any integrals along such homoclinics. All needed bounds are established using rigorous computer assisted numerics. Lastly, and most importantly, the method establishes intersections for an explicit range of parameters, and not only for perturbations that are 'small enough', as is the case in the classical Melnikov approach.
Accurate heat of formation for fully hydrided LaNi5 via the all-electron FLAPW approach
NASA Astrophysics Data System (ADS)
Zhao, Yu-Jun; Freeman, A. J.
2003-03-01
It is known that the theoretical/computational determination of the heat of formation for La_2Ni_10H_14, Δ H_f, is overestimated theoretically by 50% or more when a pseudopotential approach is employed.(Tatsumi et al), PRB 64, 184105(2001) Does this signify a failure of first-principles total energy calculations? Here, we employ the full-potential linearized augmented plane wave (FLAPW) method(Wimmer, Krakauer, Weinert, and Freeman, PRB 24), 864 (1981). within both the generalized gradient approximation (GGA) and the localized density approximation (LDA), with a highly precise treatment of the total energy of H2 molecule due to its critical role in the calculation of Δ H_f. The calculated Δ Hf (-31.1 KJ/mol-H_2) and geometry structure within GGA are in excellent agreement with experiment ( ˜ -32 KJ/mol-H_2). While LDA calculations underestimate the volume of LaNi5 by 10.4%, the final value of Δ Hf (-31.2 KJ/mol-H_2) is also in excellent agreement with experiment. These results show the success rather than failure of first-principles calculations. The electronic properties indicate that charge transfer from the interstitial region to the H atoms stabilizes the fully hydrided LaNi_5.
A computational approach for the health care market.
Montefiori, Marcello; Resta, Marina
2009-12-01
In this work we analyze the market for health care through a computational approach that relies on Kohonen's Self-Organizing Maps, and we observe the competition dynamics of health care providers versus those of patients. As a result, we offer a new tool addressing the issue of hospital behaviour and demand mechanism modelling, which conjugates a robust theoretical implementation together with an instrument of deep graphical impact.
Computer-based Approaches for Training Interactive Digital Map Displays
2005-09-01
SUPPLEMENTARY NOTES Subject Matter POC: Jean L. Dyer 14. ABSTRACT (Maximum 200 words): Five computer-based training approaches for learning digital skills...Training assessment Exploratory Learning Guided ExploratoryTraining Guided Discovery SECURITY CLASSIFICATION OF 19. LIMITATION OF 20. NUMBER 21...the other extreme of letting Soldiers learn a digital interface on their own. The research reported here examined these two conditions and three other
WSRC approach to validation of criticality safety computer codes
Finch, D.R.; Mincey, J.F.
1991-12-31
Recent hardware and operating system changes at Westinghouse Savannah River Site (WSRC) have necessitated review of the validation for JOSHUA criticality safety computer codes. As part of the planning for this effort, a policy for validation of JOSHUA and other criticality safety codes has been developed. This policy will be illustrated with the steps being taken at WSRC. The objective in validating a specific computational method is to reliably correlate its calculated neutron multiplication factor (K{sub eff}) with known values over a well-defined set of neutronic conditions. Said another way, such correlations should be: (1) repeatable; (2) demonstrated with defined confidence; and (3) identify the range of neutronic conditions (area of applicability) for which the correlations are valid. The general approach to validation of computational methods at WSRC must encompass a large number of diverse types of fissile material processes in different operations. Special problems are presented in validating computational methods when very few experiments are available (such as for enriched uranium systems with principal second isotope {sup 236}U). To cover all process conditions at WSRC, a broad validation approach has been used. Broad validation is based upon calculation of many experiments to span all possible ranges of reflection, nuclide concentrations, moderation ratios, etc. Narrow validation, in comparison, relies on calculations of a few experiments very near anticipated worst-case process conditions. The methods and problems of broad validation are discussed.
WSRC approach to validation of criticality safety computer codes
Finch, D.R.; Mincey, J.F.
1991-01-01
Recent hardware and operating system changes at Westinghouse Savannah River Site (WSRC) have necessitated review of the validation for JOSHUA criticality safety computer codes. As part of the planning for this effort, a policy for validation of JOSHUA and other criticality safety codes has been developed. This policy will be illustrated with the steps being taken at WSRC. The objective in validating a specific computational method is to reliably correlate its calculated neutron multiplication factor (K{sub eff}) with known values over a well-defined set of neutronic conditions. Said another way, such correlations should be: (1) repeatable; (2) demonstrated with defined confidence; and (3) identify the range of neutronic conditions (area of applicability) for which the correlations are valid. The general approach to validation of computational methods at WSRC must encompass a large number of diverse types of fissile material processes in different operations. Special problems are presented in validating computational methods when very few experiments are available (such as for enriched uranium systems with principal second isotope {sup 236}U). To cover all process conditions at WSRC, a broad validation approach has been used. Broad validation is based upon calculation of many experiments to span all possible ranges of reflection, nuclide concentrations, moderation ratios, etc. Narrow validation, in comparison, relies on calculations of a few experiments very near anticipated worst-case process conditions. The methods and problems of broad validation are discussed.
Archiving Software Systems: Approaches to Preserve Computational Capabilities
NASA Astrophysics Data System (ADS)
King, T. A.
2014-12-01
A great deal of effort is made to preserve scientific data. Not only because data is knowledge, but it is often costly to acquire and is sometimes collected under unique circumstances. Another part of the science enterprise is the development of software to process and analyze the data. Developed software is also a large investment and worthy of preservation. However, the long term preservation of software presents some challenges. Software often requires a specific technology stack to operate. This can include software, operating systems and hardware dependencies. One past approach to preserve computational capabilities is to maintain ancient hardware long past its typical viability. On an archive horizon of 100 years, this is not feasible. Another approach to preserve computational capabilities is to archive source code. While this can preserve details of the implementation and algorithms, it may not be possible to reproduce the technology stack needed to compile and run the resulting applications. This future forward dilemma has a solution. Technology used to create clouds and process big data can also be used to archive and preserve computational capabilities. We explore how basic hardware, virtual machines, containers and appropriate metadata can be used to preserve computational capabilities and to archive functional software systems. In conjunction with data archives, this provides scientist with both the data and capability to reproduce the processing and analysis used to generate past scientific results.
Gritzo, L.A.; Koski, J.A.; Suo-Anttila, A.J.
1999-03-16
The Container Analysis Fire Environment computer code (CAFE) is intended to provide Type B package designers with an enhanced engulfing fire boundary condition when combined with the PATRAN/P-Thermal commercial code. Historically an engulfing fire boundary condition has been modeled as {sigma}T{sup 4} where {sigma} is the Stefan-Boltzman constant, and T is the fire temperature. The CAFE code includes the necessary chemistry, thermal radiation, and fluid mechanics to model an engulfing fire. Effects included are the local cooling of gases that form a protective boundary layer that reduces the incoming radiant heat flux to values lower than expected from a simple {sigma}T{sup 4} model. In addition, the effect of object shape on mixing that may increase the local fire temperature is included. Both high and low temperature regions that depend upon the local availability of oxygen are also calculated. Thus the competing effects that can both increase and decrease the local values of radiant heat flux are included in a reamer that is not predictable a-priori. The CAFE package consists of a group of computer subroutines that can be linked to workstation-based thermal analysis codes in order to predict package performance during regulatory and other accident fire scenarios.
Gunaydin, Hakan; Acevedo, Orlando; Jorgensen, William L; Houk, K N
2007-05-01
The energetics of methyl-transfer reactions from dimethylammonium, tetramethylammonium, and trimethylsulfonium to dimethylamine were computed with density functional theory, MP2, CBS-QB3, and quantum mechanics/molecular mechanics (QM/MM) Monte Carlo methods. At the CBS-QB3 level, the gas-phase activation enthalpies are computed to be 9.9, 15.3, and 7.9 kcal/mol, respectively. MP2/6-31+G(d,p) activation enthalpies are in best agreement with the CBS-QB3 results. The effects of aqueous solvation on these reactions were studied with polarizable continuum model, generalized Born/surface area (GB/SA), and QM/MM Monte Carlo simulations utilizing free-energy perturbation theory in which the PDDG/PM3 semiempirical Hamiltonian for the QM and explicit TIP4P water molecules in the MM region were used. In the aqueous phase, all of these reactions proceed more slowly when compared to the gas phase, since the charged reactants are stabilized more than the transition structure geometries with delocalized positive charges. In order to obtain the aqueous-phase activation free energies, the gas-phase activation free energies were corrected with the solvation free energies obtained from single-point conductor-like polarizable continuum model and GB/SA calculations for the stationary points along the reaction coordinate.
Probabilistic Damage Characterization Using the Computationally-Efficient Bayesian Approach
NASA Technical Reports Server (NTRS)
Warner, James E.; Hochhalter, Jacob D.
2016-01-01
This work presents a computationally-ecient approach for damage determination that quanti es uncertainty in the provided diagnosis. Given strain sensor data that are polluted with measurement errors, Bayesian inference is used to estimate the location, size, and orientation of damage. This approach uses Bayes' Theorem to combine any prior knowledge an analyst may have about the nature of the damage with information provided implicitly by the strain sensor data to form a posterior probability distribution over possible damage states. The unknown damage parameters are then estimated based on samples drawn numerically from this distribution using a Markov Chain Monte Carlo (MCMC) sampling algorithm. Several modi cations are made to the traditional Bayesian inference approach to provide signi cant computational speedup. First, an ecient surrogate model is constructed using sparse grid interpolation to replace a costly nite element model that must otherwise be evaluated for each sample drawn with MCMC. Next, the standard Bayesian posterior distribution is modi ed using a weighted likelihood formulation, which is shown to improve the convergence of the sampling process. Finally, a robust MCMC algorithm, Delayed Rejection Adaptive Metropolis (DRAM), is adopted to sample the probability distribution more eciently. Numerical examples demonstrate that the proposed framework e ectively provides damage estimates with uncertainty quanti cation and can yield orders of magnitude speedup over standard Bayesian approaches.
NASA Astrophysics Data System (ADS)
Bermejo-Solera, Mercedes; Otero, Jesús
2009-03-01
The International GNSS Service (IGS) has been producing the total troposphere zenith path delay (ZPD) product that is based on combined ZPD contributions from several IGS Analysis Centers (AC) since GPS week 890 in 1997. A new approach to the production of the IGS ZPD has been proposed that replaces the direct combination of diverse ZPD products with point positioning estimates using the IGS Combined Final orbit and clock products. The new product was formally adopted in 2007 after several years of concurrent production with the legacy product. We describe here the advantages of the new approach for the IGS ZPD product, which enhance the value of the new ZPD product for climate studies. We also address the impact the IGS adoption in November 2006 of new GPS antenna phase center standards has had on the new ZPD product. Finally we describe plans to further enhance the ZPD products.
A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems.
Factorovich, Matías H; Molinero, Valeria; Scherlis, Damián A
2014-02-14
In this article we introduce a simple grand canonical screening (GCS) approach to accurately compute vapor pressures from molecular dynamics or Monte Carlo simulations. This procedure entails a screening of chemical potentials using a conventional grand canonical scheme, and therefore it is straightforward to implement for any kind of interface. The scheme is validated against data obtained from Gibbs ensemble simulations for water and argon. Then, it is applied to obtain the vapor pressure of the coarse-grained mW water model, and it is shown that the computed value is in excellent accord with the one formally deduced using statistical thermodynamics arguments. Finally, this methodology is used to calculate the vapor pressure of a water nanodroplet of 94 molecules. Interestingly, the result is in perfect agreement with the one predicted by the Kelvin equation for a homogeneous droplet of that size.
A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems
Factorovich, Matías H.; Scherlis, Damián A.
2014-02-14
In this article we introduce a simple grand canonical screening (GCS) approach to accurately compute vapor pressures from molecular dynamics or Monte Carlo simulations. This procedure entails a screening of chemical potentials using a conventional grand canonical scheme, and therefore it is straightforward to implement for any kind of interface. The scheme is validated against data obtained from Gibbs ensemble simulations for water and argon. Then, it is applied to obtain the vapor pressure of the coarse-grained mW water model, and it is shown that the computed value is in excellent accord with the one formally deduced using statistical thermodynamics arguments. Finally, this methodology is used to calculate the vapor pressure of a water nanodroplet of 94 molecules. Interestingly, the result is in perfect agreement with the one predicted by the Kelvin equation for a homogeneous droplet of that size.
Pires, Douglas E V; Ascher, David B; Blundell, Tom L
2014-07-01
Cancer genome and other sequencing initiatives are generating extensive data on non-synonymous single nucleotide polymorphisms (nsSNPs) in human and other genomes. In order to understand the impacts of nsSNPs on the structure and function of the proteome, as well as to guide protein engineering, accurate in silicomethodologies are required to study and predict their effects on protein stability. Despite the diversity of available computational methods in the literature, none has proven accurate and dependable on its own under all scenarios where mutation analysis is required. Here we present DUET, a web server for an integrated computational approach to study missense mutations in proteins. DUET consolidates two complementary approaches (mCSM and SDM) in a consensus prediction, obtained by combining the results of the separate methods in an optimized predictor using Support Vector Machines (SVM). We demonstrate that the proposed method improves overall accuracy of the predictions in comparison with either method individually and performs as well as or better than similar methods. The DUET web server is freely and openly available at http://structure.bioc.cam.ac.uk/duet.
A Computer Vision Approach to Identify Einstein Rings and Arcs
NASA Astrophysics Data System (ADS)
Lee, Chien-Hsiu
2017-03-01
Einstein rings are rare gems of strong lensing phenomena; the ring images can be used to probe the underlying lens gravitational potential at every position angles, tightly constraining the lens mass profile. In addition, the magnified images also enable us to probe high-z galaxies with enhanced resolution and signal-to-noise ratios. However, only a handful of Einstein rings have been reported, either from serendipitous discoveries or or visual inspections of hundred thousands of massive galaxies or galaxy clusters. In the era of large sky surveys, an automated approach to identify ring pattern in the big data to come is in high demand. Here, we present an Einstein ring recognition approach based on computer vision techniques. The workhorse is the circle Hough transform that recognise circular patterns or arcs in the images. We propose a two-tier approach by first pre-selecting massive galaxies associated with multiple blue objects as possible lens, than use Hough transform to identify circular pattern. As a proof-of-concept, we apply our approach to SDSS, with a high completeness, albeit with low purity. We also apply our approach to other lenses in DES, HSC-SSP, and UltraVISTA survey, illustrating the versatility of our approach.
Computational neuroscience approach to biomarkers and treatments for mental disorders.
Yahata, Noriaki; Kasai, Kiyoto; Kawato, Mitsuo
2017-04-01
Psychiatry research has long experienced a stagnation stemming from a lack of understanding of the neurobiological underpinnings of phenomenologically defined mental disorders. Recently, the application of computational neuroscience to psychiatry research has shown great promise in establishing a link between phenomenological and pathophysiological aspects of mental disorders, thereby recasting current nosology in more biologically meaningful dimensions. In this review, we highlight recent investigations into computational neuroscience that have undertaken either theory- or data-driven approaches to quantitatively delineate the mechanisms of mental disorders. The theory-driven approach, including reinforcement learning models, plays an integrative role in this process by enabling correspondence between behavior and disorder-specific alterations at multiple levels of brain organization, ranging from molecules to cells to circuits. Previous studies have explicated a plethora of defining symptoms of mental disorders, including anhedonia, inattention, and poor executive function. The data-driven approach, on the other hand, is an emerging field in computational neuroscience seeking to identify disorder-specific features among high-dimensional big data. Remarkably, various machine-learning techniques have been applied to neuroimaging data, and the extracted disorder-specific features have been used for automatic case-control classification. For many disorders, the reported accuracies have reached 90% or more. However, we note that rigorous tests on independent cohorts are critically required to translate this research into clinical applications. Finally, we discuss the utility of the disorder-specific features found by the data-driven approach to psychiatric therapies, including neurofeedback. Such developments will allow simultaneous diagnosis and treatment of mental disorders using neuroimaging, thereby establishing 'theranostics' for the first time in clinical
Computational approaches to parameter estimation and model selection in immunology
NASA Astrophysics Data System (ADS)
Baker, C. T. H.; Bocharov, G. A.; Ford, J. M.; Lumb, P. M.; Norton, S. J.; Paul, C. A. H.; Junt, T.; Krebs, P.; Ludewig, B.
2005-12-01
One of the significant challenges in biomathematics (and other areas of science) is to formulate meaningful mathematical models. Our problem is to decide on a parametrized model which is, in some sense, most likely to represent the information in a set of observed data. In this paper, we illustrate the computational implementation of an information-theoretic approach (associated with a maximum likelihood treatment) to modelling in immunology.The approach is illustrated by modelling LCMV infection using a family of models based on systems of ordinary differential and delay differential equations. The models (which use parameters that have a scientific interpretation) are chosen to fit data arising from experimental studies of virus-cytotoxic T lymphocyte kinetics; the parametrized models that result are arranged in a hierarchy by the computation of Akaike indices. The practical illustration is used to convey more general insight. Because the mathematical equations that comprise the models are solved numerically, the accuracy in the computation has a bearing on the outcome, and we address this and other practical details in our discussion.
Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches
Beatty, Perrin H.; Klein, Matthias S.; Fischer, Jeffrey J.; Lewis, Ian A.; Muench, Douglas G.; Good, Allen G.
2016-01-01
A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields. PMID:27735856
A grid computing-based approach for the acceleration of simulations in cardiology.
Alonso, José M; Ferrero, José M; Hernández, Vicente; Moltó, Germán; Saiz, Javier; Trénor, Beatriz
2008-03-01
This paper combines high-performance computing and grid computing technologies to accelerate multiple executions of a biomedical application that simulates the action potential propagation on cardiac tissues. First, a parallelization strategy was employed to accelerate the execution of simulations on a cluster of personal computers (PCs). Then, grid computing was employed to concurrently perform the multiple simulations that compose the cardiac case studies on the resources of a grid deployment, by means of a service-oriented approach. This way, biomedical experts are provided with a gateway to easily access a grid infrastructure for the execution of these research studies. Emphasis is stressed on the methodology employed. In order to assess the benefits of the grid, a cardiac case study, which analyzes the effects of premature stimulation on reentry generation during myocardial ischemia, has been carried out. The collaborative usage of a distributed computing infrastructure has reduced the time required for the execution of cardiac case studies, which allows, for example, to take more accurate decisions when evaluating the effects of new antiarrhythmic drugs on the electrical activity of the heart.
Geng, Jiun-Hung; Tu, Hung-Pin; Shih, Paul Ming-Chen; Shen, Jung-Tsung; Jang, Mei-Yu; Wu, Wen-Jen; Li, Ching-Chia; Chou, Yii-Her; Juan, Yung-Shun
2015-01-01
Urolithiasis is a common disease of the urinary system. Extracorporeal shockwave lithotripsy (SWL) has become one of the standard treatments for renal and ureteral stones; however, the success rates range widely and failure of stone disintegration may cause additional outlay, alternative procedures, and even complications. We used the data available from noncontrast abdominal computed tomography (NCCT) to evaluate the impact of stone parameters and abdominal fat distribution on calculus-free rates following SWL. We retrospectively reviewed 328 patients who had urinary stones and had undergone SWL from August 2012 to August 2013. All of them received pre-SWL NCCT; 1 month after SWL, radiography was arranged to evaluate the condition of the fragments. These patients were classified into stone-free group and residual stone group. Unenhanced computed tomography variables, including stone attenuation, abdominal fat area, and skin-to-stone distance (SSD) were analyzed. In all, 197 (60%) were classified as stone-free and 132 (40%) as having residual stone. The mean ages were 49.35 ± 13.22 years and 55.32 ± 13.52 years, respectively. On univariate analysis, age, stone size, stone surface area, stone attenuation, SSD, total fat area (TFA), abdominal circumference, serum creatinine, and the severity of hydronephrosis revealed statistical significance between these two groups. From multivariate logistic regression analysis, the independent parameters impacting SWL outcomes were stone size, stone attenuation, TFA, and serum creatinine. [Adjusted odds ratios and (95% confidence intervals): 9.49 (3.72-24.20), 2.25 (1.22-4.14), 2.20 (1.10-4.40), and 2.89 (1.35-6.21) respectively, all p < 0.05]. In the present study, stone size, stone attenuation, TFA and serum creatinine were four independent predictors for stone-free rates after SWL. These findings suggest that pretreatment NCCT may predict the outcomes after SWL. Consequently, we can use these predictors for selecting
A GPU-computing Approach to Solar Stokes Profile Inversion
NASA Astrophysics Data System (ADS)
Harker, Brian J.; Mighell, Kenneth J.
2012-09-01
We present a new computational approach to the inversion of solar photospheric Stokes polarization profiles, under the Milne-Eddington model, for vector magnetography. Our code, named GENESIS, employs multi-threaded parallel-processing techniques to harness the computing power of graphics processing units (GPUs), along with algorithms designed to exploit the inherent parallelism of the Stokes inversion problem. Using a genetic algorithm (GA) engineered specifically for use with a GPU, we produce full-disk maps of the photospheric vector magnetic field from polarized spectral line observations recorded by the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) instrument. We show the advantages of pairing a population-parallel GA with data-parallel GPU-computing techniques, and present an overview of the Stokes inversion problem, including a description of our adaptation to the GPU-computing paradigm. Full-disk vector magnetograms derived by this method are shown using SOLIS/VSM data observed on 2008 March 28 at 15:45 UT.
Computing electronic structures: A new multiconfiguration approach for excited states
NASA Astrophysics Data System (ADS)
Cancès, Éric; Galicher, Hervé; Lewin, Mathieu
2006-02-01
We present a new method for the computation of electronic excited states of molecular systems. This method is based upon a recent theoretical definition of multiconfiguration excited states [due to one of us, see M. Lewin, Solutions of the multiconfiguration equations in quantum chemistry, Arch. Rat. Mech. Anal. 171 (2004) 83-114]. Our algorithm, dedicated to the computation of the first excited state, always converges to a stationary state of the multiconfiguration model, which can be interpreted as an approximate excited state of the molecule. The definition of this approximate excited state is variational. An interesting feature is that it satisfies a non-linear Hylleraas-Undheim-MacDonald type principle: the energy of the approximate excited state is an upper bound to the true excited state energy of the N-body Hamiltonian. To compute the first excited state, one has to deform paths on a manifold, like this is usually done in the search for transition states between reactants and products on potential energy surfaces. We propose here a general method for the deformation of paths which could also be useful in other settings. We also compare our method to other approaches used in Quantum Chemistry and give some explanation of the unsatisfactory behaviours which are sometimes observed when using the latters. Numerical results for the special case of two-electron systems are provided: we compute the first singlet excited state potential energy surface of the H2 molecule.
Computational approaches in the design of synthetic receptors - A review.
Cowen, Todd; Karim, Kal; Piletsky, Sergey
2016-09-14
The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as "plastic antibodies" - high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller-Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology.
Computing electronic structures: A new multiconfiguration approach for excited states
Cances, Eric . E-mail: cances@cermics.enpc.fr; Galicher, Herve . E-mail: galicher@cermics.enpc.fr; Lewin, Mathieu . E-mail: lewin@cermic.enpc.fr
2006-02-10
We present a new method for the computation of electronic excited states of molecular systems. This method is based upon a recent theoretical definition of multiconfiguration excited states [due to one of us, see M. Lewin, Solutions of the multiconfiguration equations in quantum chemistry, Arch. Rat. Mech. Anal. 171 (2004) 83-114]. Our algorithm, dedicated to the computation of the first excited state, always converges to a stationary state of the multiconfiguration model, which can be interpreted as an approximate excited state of the molecule. The definition of this approximate excited state is variational. An interesting feature is that it satisfies a non-linear Hylleraas-Undheim-MacDonald type principle: the energy of the approximate excited state is an upper bound to the true excited state energy of the N-body Hamiltonian. To compute the first excited state, one has to deform paths on a manifold, like this is usually done in the search for transition states between reactants and products on potential energy surfaces. We propose here a general method for the deformation of paths which could also be useful in other settings. We also compare our method to other approaches used in Quantum Chemistry and give some explanation of the unsatisfactory behaviours which are sometimes observed when using the latter. Numerical results for the special case of two-electron systems are provided: we compute the first singlet excited state potential energy surface of the H {sub 2} molecule.
Alecu, I. M.; Truhlar, D. G.
2011-04-07
The reactions of CH_{3}OH with the HO_{2} and CH_{3} radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)_{Q}), core–valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol^{-1} agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.
Bedogni, Alberto; Fedele, Stefano; Bedogni, Giorgio; Scoletta, Matteo; Favia, Gianfranco; Colella, Giuseppe; Agrillo, Alessandro; Bettini, Giordana; Di Fede, Olga; Oteri, Giacomo; Fusco, Vittorio; Gabriele, Mario; Ottolenghi, Livia; Valsecchi, Stefano; Porter, Stephen; Petruzzi, Massimo; Arduino, Paolo; D'Amato, Salvatore; Ungari, Claudio; Fung Polly, Pok-Lam; Saia, Giorgia; Campisi, Giuseppina
2014-09-01
Management of osteonecrosis of the jaw associated with antiresorptive agents is challenging, and outcomes are unpredictable. The severity of disease is the main guide to management, and can help to predict prognosis. Most available staging systems for osteonecrosis, including the widely-used American Association of Oral and Maxillofacial Surgeons (AAOMS) system, classify severity on the basis of clinical and radiographic findings. However, clinical inspection and radiography are limited in their ability to identify the extent of necrotic bone disease compared with computed tomography (CT). We have organised a large multicentre retrospective study (known as MISSION) to investigate the agreement between the AAOMS staging system and the extent of osteonecrosis of the jaw (focal compared with diffuse involvement of bone) as detected on CT. We studied 799 patients with detailed clinical phenotyping who had CT images taken. Features of diffuse bone disease were identified on CT within all AAOMS stages (20%, 8%, 48%, and 24% of patients in stages 0, 1, 2, and 3, respectively). Of the patients classified as stage 0, 110/192 (57%) had diffuse disease on CT, and about 1 in 3 with CT evidence of diffuse bone disease was misclassified by the AAOMS system as having stages 0 and 1 osteonecrosis. In addition, more than a third of patients with AAOMS stage 2 (142/405, 35%) had focal bone disease on CT. We conclude that the AAOMS staging system does not correctly identify the extent of bony disease in patients with osteonecrosis of the jaw.
Ha, Tae Kyung; Choi, Yun Young; Song, Soon Young
2011-01-01
Purpose To investigate the clinical benefits of F18-fluorodeoxyglucose-positron emission tomography and computed tomography (18F-FDG-PET/CT) over multi-detector row CT (MDCT) in preoperative staging of gastric cancer. Methods FDG-PET/CT and MDCT were performed on 78 patients with gastric cancer pathologically diagnosed by endoscopy. The accuracy of radiologic staging retrospectively was compared to pathologic result after curative resection. Results Primary tumors were detected in 51 (65.4%) patients with 18F-FDG-PET/CT, and 47 (60.3%) patients with MDCT. Regarding detection of lymph node metastasis, the sensitivity of FDG-PET/CT was 51.5% with an accuracy of 71.8%, whereas those of MDCT were 69.7% and 69.2%, respectively. The sensitivity of 18F-FDG-PET/CT for a primary tumor with signet ring cell carcinoma was lower than that of 18F-FDG-PET/CT for a primary tumor with non-signet ring cell carcinoma (35.3% vs. 73.8%, P < 0.01). Conclusion Due to its low sensitivity, 18F-FDG-PET/CT alone shows no definite clinical benefit for prediction of lymph node metastasis in preoperative staging of gastric cancer. PMID:22066108
Computational modeling of an endovascular approach to deep brain stimulation
NASA Astrophysics Data System (ADS)
Teplitzky, Benjamin A.; Connolly, Allison T.; Bajwa, Jawad A.; Johnson, Matthew D.
2014-04-01
Objective. Deep brain stimulation (DBS) therapy currently relies on a transcranial neurosurgical technique to implant one or more electrode leads into the brain parenchyma. In this study, we used computational modeling to investigate the feasibility of using an endovascular approach to target DBS therapy. Approach. Image-based anatomical reconstructions of the human brain and vasculature were used to identify 17 established and hypothesized anatomical targets of DBS, of which five were found adjacent to a vein or artery with intraluminal diameter ≥1 mm. Two of these targets, the fornix and subgenual cingulate white matter (SgCwm) tracts, were further investigated using a computational modeling framework that combined segmented volumes of the vascularized brain, finite element models of the tissue voltage during DBS, and multi-compartment axon models to predict the direct electrophysiological effects of endovascular DBS. Main results. The models showed that: (1) a ring-electrode conforming to the vessel wall was more efficient at neural activation than a guidewire design, (2) increasing the length of a ring-electrode had minimal effect on neural activation thresholds, (3) large variability in neural activation occurred with suboptimal placement of a ring-electrode along the targeted vessel, and (4) activation thresholds for the fornix and SgCwm tracts were comparable for endovascular and stereotactic DBS, though endovascular DBS was able to produce significantly larger contralateral activation for a unilateral implantation. Significance. Together, these results suggest that endovascular DBS can serve as a complementary approach to stereotactic DBS in select cases.
An alternative approach for computing seismic response with accidental eccentricity
NASA Astrophysics Data System (ADS)
Fan, Xuanhua; Yin, Jiacong; Sun, Shuli; Chen, Pu
2014-09-01
Accidental eccentricity is a non-standard assumption for seismic design of tall buildings. Taking it into consideration requires reanalysis of seismic resistance, which requires either time consuming computation of natural vibration of eccentric structures or finding a static displacement solution by applying an approximated equivalent torsional moment for each eccentric case. This study proposes an alternative modal response spectrum analysis (MRSA) approach to calculate seismic responses with accidental eccentricity. The proposed approach, called the Rayleigh Ritz Projection-MRSA (RRP-MRSA), is developed based on MRSA and two strategies: (a) a RRP method to obtain a fast calculation of approximate modes of eccentric structures; and (b) an approach to assemble mass matrices of eccentric structures. The efficiency of RRP-MRSA is tested via engineering examples and compared with the standard MRSA (ST-MRSA) and one approximate method, i.e., the equivalent torsional moment hybrid MRSA (ETM-MRSA). Numerical results show that RRP-MRSA not only achieves almost the same precision as ST-MRSA, and is much better than ETM-MRSA, but is also more economical. Thus, RRP-MRSA can be in place of current accidental eccentricity computations in seismic design.
Thomas, Peter B. M.; Baltrušaitis, Tadas; Robinson, Peter; Vivian, Anthony J.
2016-01-01
Purpose We validate a video-based method of head posture measurement. Methods The Cambridge Face Tracker uses neural networks (constrained local neural fields) to recognize facial features in video. The relative position of these facial features is used to calculate head posture. First, we assess the accuracy of this approach against videos in three research databases where each frame is tagged with a precisely measured head posture. Second, we compare our method to a commercially available mechanical device, the Cervical Range of Motion device: four subjects each adopted 43 distinct head postures that were measured using both methods. Results The Cambridge Face Tracker achieved confident facial recognition in 92% of the approximately 38,000 frames of video from the three databases. The respective mean error in absolute head posture was 3.34°, 3.86°, and 2.81°, with a median error of 1.97°, 2.16°, and 1.96°. The accuracy decreased with more extreme head posture. Comparing The Cambridge Face Tracker to the Cervical Range of Motion Device gave correlation coefficients of 0.99 (P < 0.0001), 0.96 (P < 0.0001), and 0.99 (P < 0.0001) for yaw, pitch, and roll, respectively. Conclusions The Cambridge Face Tracker performs well under real-world conditions and within the range of normally-encountered head posture. It allows useful quantification of head posture in real time or from precaptured video. Its performance is similar to that of a clinically validated mechanical device. It has significant advantages over other approaches in that subjects do not need to wear any apparatus, and it requires only low cost, easy-to-setup consumer electronics. Translational Relevance Noncontact assessment of head posture allows more complete clinical assessment of patients, and could benefit surgical planning in future. PMID:27730008
[Computer work and De Quervain's tenosynovitis: an evidence based approach].
Gigante, M R; Martinotti, I; Cirla, P E
2012-01-01
The debate around the role of the work at personal computer as cause of De Quervain's Tenosynovitis was developed partially, without considering multidisciplinary available data. A systematic review of the literature, using an evidence-based approach, was performed. In disorders associated with the use of VDU, we must distinguish those at the upper limbs and among them those related to an overload. Experimental studies on the occurrence of De Quervain's Tenosynovitis are quite limited, as well as clinically are quite difficult to prove the professional etiology, considering the interference due to other activities of daily living or to the biological susceptibility (i.e. anatomical variability, sex, age, exercise). At present there is no evidence of any connection between De Quervain syndrome and time of use of the personal computer or keyboard, limited evidence of correlation is found with time using a mouse. No data are available regarding the use exclusively or predominantly for personal laptops or mobile "smart phone".
Slide Star: An Approach to Videodisc/Computer Aided Instruction
McEnery, Kevin W.
1984-01-01
One of medical education's primary goals is for the student to be proficient in the gross and microscopic identification of disease. The videodisc, with its storage capacity of up to 54,000 photomicrographs is ideally suited to assist in this educational process. “Slide Star” is a method of interactive instruction which is designed for use in any subject where it is essential to identify visual material. The instructional approach utilizes a computer controlled videodisc to display photomicrographs. In the demonstration program, these are slides of normal blood cells. The program is unique in that the instruction is created by the student's commands manipulating the photomicrograph data base. A prime feature is the use of computer generated multiple choice questions to reinforce the learning process.
Analytical and computational approaches to define the Aspergillus niger secretome
Tsang, Adrian; Butler, Gregory D.; Powlowski, Justin; Panisko, Ellen A.; Baker, Scott E.
2009-03-01
We used computational and mass spectrometric approaches to characterize the Aspergillus niger secretome. The 11,200 gene models predicted in the genome of A. niger strain ATCC 1015 were the data source for the analysis. Depending on the computational methods used, 691 to 881 proteins were predicted to be secreted proteins. We cultured A. niger in six different media and analyzed the extracellular proteins produced using mass spectrometry. A total of 222 proteins were identified, with 39 proteins expressed under all six conditions and 74 proteins expressed under only one condition. The secreted proteins identified by mass spectrometry were used to guide the correction of about 20 gene models. Additional analysis focused on extracellular enzymes of interest for biomass processing. Of the 63 glycoside hydrolases predicted to be capable of hydrolyzing cellulose, hemicellulose or pectin, 94% of the exo-acting enzymes and only 18% of the endo-acting enzymes were experimentally detected.
A Computational Approach for Probabilistic Analysis of Water Impact Simulations
NASA Technical Reports Server (NTRS)
Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.
2009-01-01
NASA's development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.
Computational approaches for rational design of proteins with novel functionalities
Tiwari, Manish Kumar; Singh, Ranjitha; Singh, Raushan Kumar; Kim, In-Won; Lee, Jung-Kul
2012-01-01
Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has numerous potential applications. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. The field of de novo protein design, although only a few decades old, is beginning to produce exciting results. Developments in this field are already having a significant impact on biotechnology and chemical biology. The application of powerful computational methods for functional protein designing has recently succeeded at engineering target activities. Here, we review recently reported de novo functional proteins that were developed using various protein design approaches, including rational design, computational optimization, and selection from combinatorial libraries, highlighting recent advances and successes. PMID:24688643
A pencil beam approach to proton computed tomography
Rescigno, Regina Bopp, Cécile; Rousseau, Marc; Brasse, David
2015-11-15
Purpose: A new approach to proton computed tomography (pCT) is presented. In this approach, protons are not tracked one-by-one but a beam of particles is considered instead. The elements of the pCT reconstruction problem (residual energy and path) are redefined on the basis of this new approach. An analytical image reconstruction algorithm applicable to this scenario is also proposed. Methods: The pencil beam (PB) and its propagation in matter were modeled by making use of the generalization of the Fermi–Eyges theory to account for multiple Coulomb scattering (MCS). This model was integrated into the pCT reconstruction problem, allowing the definition of the mean beam path concept similar to the most likely path (MLP) used in the single-particle approach. A numerical validation of the model was performed. The algorithm of filtered backprojection along MLPs was adapted to the beam-by-beam approach. The acquisition of a perfect proton scan was simulated and the data were used to reconstruct images of the relative stopping power of the phantom with the single-proton and beam-by-beam approaches. The resulting images were compared in a qualitative way. Results: The parameters of the modeled PB (mean and spread) were compared to Monte Carlo results in order to validate the model. For a water target, good agreement was found for the mean value of the distributions. As far as the spread is concerned, depth-dependent discrepancies as large as 2%–3% were found. For a heterogeneous phantom, discrepancies in the distribution spread ranged from 6% to 8%. The image reconstructed with the beam-by-beam approach showed a high level of noise compared to the one reconstructed with the classical approach. Conclusions: The PB approach to proton imaging may allow technical challenges imposed by the current proton-by-proton method to be overcome. In this framework, an analytical algorithm is proposed. Further work will involve a detailed study of the performances and limitations of
The process group approach to reliable distributed computing
NASA Technical Reports Server (NTRS)
Birman, Kenneth P.
1991-01-01
The difficulty of developing reliable distributed software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems which are substantially easier to develop, fault-tolerance, and self-managing. Six years of research on ISIS are reviewed, describing the model, the types of applications to which ISIS was applied, and some of the reasoning that underlies a recent effort to redesign and reimplement ISIS as a much smaller, lightweight system.
Physiologically based computational approach to camouflage and masking patterns
NASA Astrophysics Data System (ADS)
Irvin, Gregg E.; Dowler, Michael G.
1992-09-01
A computational system was developed to integrate both Fourier image processing techniques and biologically based image processing techniques. The Fourier techniques allow the spatially global manipulation of phase and amplitude spectra. The biologically based techniques allow for spatially localized manipulation of phase, amplitude and orientation independently on multiple spatial frequency scales. These techniques combined with a large variety of basic image processing functions allow for a versatile and systematic approach to be taken toward the development of specialized patterning and visual textures. Current applications involve research for the development of 2-dimensional spatial patterning that can function as effective camouflage patterns and masking patterns for the human visual system.
Approaches to Computer Modeling of Phosphate Hide-Out.
1984-06-28
phosphate acts as a buffer to keep pH at a value above which acid corrosion occurs . and below which caustic corrosion becomes significant. Difficulties are...ionization of dihydrogen phosphate : HIPO - + + 1PO, K (B-7) H+ + - £Iao 1/1, (B-8) H , PO4 - + O- - H0 4 + H20 K/Kw (0-9) 19 * Such zero heat...OF STANDARDS-1963-A +. .0 0 0 9t~ - 4 NRL Memorandum Report 5361 4 Approaches to Computer Modeling of Phosphate Hide-Out K. A. S. HARDY AND J. C
Identification of Protein–Excipient Interaction Hotspots Using Computational Approaches
Barata, Teresa S.; Zhang, Cheng; Dalby, Paul A.; Brocchini, Steve; Zloh, Mire
2016-01-01
Protein formulation development relies on the selection of excipients that inhibit protein–protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein–excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein–protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations. PMID:27258262
A Computational Approach for Identifying Synergistic Drug Combinations
Gayvert, Kaitlyn M.; Aly, Omar; Bosenberg, Marcus W.; Stern, David F.; Elemento, Olivier
2017-01-01
A promising alternative to address the problem of acquired drug resistance is to rely on combination therapies. Identification of the right combinations is often accomplished through trial and error, a labor and resource intensive process whose scale quickly escalates as more drugs can be combined. To address this problem, we present a broad computational approach for predicting synergistic combinations using easily obtainable single drug efficacy, no detailed mechanistic understanding of drug function, and limited drug combination testing. When applied to mutant BRAF melanoma, we found that our approach exhibited significant predictive power. Additionally, we validated previously untested synergy predictions involving anticancer molecules. As additional large combinatorial screens become available, this methodology could prove to be impactful for identification of drug synergy in context of other types of cancers. PMID:28085880
Stochastic Computational Approach for Complex Nonlinear Ordinary Differential Equations
NASA Astrophysics Data System (ADS)
Junaid, Ali Khan; Muhammad, Asif Zahoor Raja; Ijaz Mansoor, Qureshi
2011-02-01
We present an evolutionary computational approach for the solution of nonlinear ordinary differential equations (NLODEs). The mathematical modeling is performed by a feed-forward artificial neural network that defines an unsupervised error. The training of these networks is achieved by a hybrid intelligent algorithm, a combination of global search with genetic algorithm and local search by pattern search technique. The applicability of this approach ranges from single order NLODEs, to systems of coupled differential equations. We illustrate the method by solving a variety of model problems and present comparisons with solutions obtained by exact methods and classical numerical methods. The solution is provided on a continuous finite time interval unlike the other numerical techniques with comparable accuracy. With the advent of neuroprocessors and digital signal processors the method becomes particularly interesting due to the expected essential gains in the execution speed.
Crowd Computing as a Cooperation Problem: An Evolutionary Approach
NASA Astrophysics Data System (ADS)
Christoforou, Evgenia; Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Sánchez, Angel
2013-05-01
Cooperation is one of the socio-economic issues that has received more attention from the physics community. The problem has been mostly considered by studying games such as the Prisoner's Dilemma or the Public Goods Game. Here, we take a step forward by studying cooperation in the context of crowd computing. We introduce a model loosely based on Principal-agent theory in which people (workers) contribute to the solution of a distributed problem by computing answers and reporting to the problem proposer (master). To go beyond classical approaches involving the concept of Nash equilibrium, we work on an evolutionary framework in which both the master and the workers update their behavior through reinforcement learning. Using a Markov chain approach, we show theoretically that under certain----not very restrictive—conditions, the master can ensure the reliability of the answer resulting of the process. Then, we study the model by numerical simulations, finding that convergence, meaning that the system reaches a point in which it always produces reliable answers, may in general be much faster than the upper bounds given by the theoretical calculation. We also discuss the effects of the master's level of tolerance to defectors, about which the theory does not provide information. The discussion shows that the system works even with very large tolerances. We conclude with a discussion of our results and possible directions to carry this research further.
Learning about modes of speciation by computational approaches.
Becquet, Céline; Przeworski, Molly
2009-10-01
How often do the early stages of speciation occur in the presence of gene flow? To address this enduring question, a number of recent papers have used computational approaches, estimating parameters of simple divergence models from multilocus polymorphism data collected in closely related species. Applications to a variety of species have yielded extensive evidence for migration, with the results interpreted as supporting the widespread occurrence of parapatric speciation. Here, we conduct a simulation study to assess the reliability of such inferences, using a program that we recently developed MCMC estimation of the isolation-migration model allowing for recombination (MIMAR) as well as the program isolation-migration (IM) of Hey and Nielsen (2004). We find that when one of many assumptions of the isolation-migration model is violated, the methods tend to yield biased estimates of the parameters, potentially lending spurious support for allopatric or parapatric divergence. More generally, our results highlight the difficulty in drawing inferences about modes of speciation from the existing computational approaches alone.
Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis
Bokota, Grzegorz; Magnowska, Marta; Kuśmierczyk, Tomasz; Łukasik, Michał; Roszkowska, Matylda; Plewczynski, Dariusz
2016-01-01
The common approach in morphological analysis of dendritic spines of mammalian neuronal cells is to categorize spines into subpopulations based on whether they are stubby, mushroom, thin, or filopodia shaped. The corresponding cellular models of synaptic plasticity, long-term potentiation, and long-term depression associate the synaptic strength with either spine enlargement or spine shrinkage. Although a variety of automatic spine segmentation and feature extraction methods were developed recently, no approaches allowing for an automatic and unbiased distinction between dendritic spine subpopulations and detailed computational models of spine behavior exist. We propose an automatic and statistically based method for the unsupervised construction of spine shape taxonomy based on arbitrary features. The taxonomy is then utilized in the newly introduced computational model of behavior, which relies on transitions between shapes. Models of different populations are compared using supplied bootstrap-based statistical tests. We compared two populations of spines at two time points. The first population was stimulated with long-term potentiation, and the other in the resting state was used as a control. The comparison of shape transition characteristics allowed us to identify the differences between population behaviors. Although some extreme changes were observed in the stimulated population, statistically significant differences were found only when whole models were compared. The source code of our software is freely available for non-commercial use1. Contact: d.plewczynski@cent.uw.edu.pl. PMID:28066226
Computational approaches to understand cardiac electrophysiology and arrhythmias
Roberts, Byron N.; Yang, Pei-Chi; Behrens, Steven B.; Moreno, Jonathan D.
2012-01-01
Cardiac rhythms arise from electrical activity generated by precisely timed opening and closing of ion channels in individual cardiac myocytes. These impulses spread throughout the cardiac muscle to manifest as electrical waves in the whole heart. Regularity of electrical waves is critically important since they signal the heart muscle to contract, driving the primary function of the heart to act as a pump and deliver blood to the brain and vital organs. When electrical activity goes awry during a cardiac arrhythmia, the pump does not function, the brain does not receive oxygenated blood, and death ensues. For more than 50 years, mathematically based models of cardiac electrical activity have been used to improve understanding of basic mechanisms of normal and abnormal cardiac electrical function. Computer-based modeling approaches to understand cardiac activity are uniquely helpful because they allow for distillation of complex emergent behaviors into the key contributing components underlying them. Here we review the latest advances and novel concepts in the field as they relate to understanding the complex interplay between electrical, mechanical, structural, and genetic mechanisms during arrhythmia development at the level of ion channels, cells, and tissues. We also discuss the latest computational approaches to guiding arrhythmia therapy. PMID:22886409
Computational inference of gene regulatory networks: Approaches, limitations and opportunities.
Banf, Michael; Rhee, Seung Y
2017-01-01
Gene regulatory networks lie at the core of cell function control. In E. coli and S. cerevisiae, the study of gene regulatory networks has led to the discovery of regulatory mechanisms responsible for the control of cell growth, differentiation and responses to environmental stimuli. In plants, computational rendering of gene regulatory networks is gaining momentum, thanks to the recent availability of high-quality genomes and transcriptomes and development of computational network inference approaches. Here, we review current techniques, challenges and trends in gene regulatory network inference and highlight challenges and opportunities for plant science. We provide plant-specific application examples to guide researchers in selecting methodologies that suit their particular research questions. Given the interdisciplinary nature of gene regulatory network inference, we tried to cater to both biologists and computer scientists to help them engage in a dialogue about concepts and caveats in network inference. Specifically, we discuss problems and opportunities in heterogeneous data integration for eukaryotic organisms and common caveats to be considered during network model evaluation. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Scalable, massively parallel approaches to upstream drainage area computation
NASA Astrophysics Data System (ADS)
Richardson, A.; Hill, C. N.; Perron, T.
2011-12-01
Accumulated drainage area maps of large regions are required for several applications. Among these are assessments of regional patterns of flow and sediment routing, high-resolution landscape evolution models in which drainage basin geometry evolves with time, and surveys of the characteristics of river basins that drain to continental margins. The computation of accumulated drainage areas is accomplished by inferring the vector field of drainage flow directions from a two-dimensional digital elevation map, and then computing the area that drains to each tile. From this map of elevations we can compute the integrated, upstream area that drains to each tile of the map. Generally this last step is done with a recursive algorithm, that accumulates upstream areas sequentially. The inherently serial nature of this restricts the number of tiles that can be included, thereby limiting the resolution of continental-size domains. This is because of the requirements of both memory, which will rise proportionally to the number of tiles, N, and computing time, which is O(N2). The fundamental sequential property of this approach prohibits effective use of large scale parallelism. An alternate method of calculating accumulated drainage area from drainage direction data can be arrived at by reformulating the problem as the solution of a system of simultaneous linear equations. The equations define the relation that the total upslope area of a particular tile is the sum of all the upslope areas for tiles immediately adjacent to that tile that drain to it, and the tile's own area. Solving these equations amounts to finding the solution of a sparse, nine-diagonal matrix operating on a vector for a right-hand-side that is simply the individual tile areas and where the diagonals of the matrix are determined by the landscape geometry. We show how an iterative method, Bi-CGSTAB, can be used to solve this problem in a scalable, massively parallel manner. However, this introduces
Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations
NASA Astrophysics Data System (ADS)
Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying
2010-09-01
Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).
A Resampling Based Approach to Optimal Experimental Design for Computer Analysis of a Complex System
Rutherford, Brian
1999-08-04
The investigation of a complex system is often performed using computer generated response data supplemented by system and component test results where possible. Analysts rely on an efficient use of limited experimental resources to test the physical system, evaluate the models and to assure (to the extent possible) that the models accurately simulate the system order investigation. The general problem considered here is one where only a restricted number of system simulations (or physical tests) can be performed to provide additional data necessary to accomplish the project objectives. The levels of variables used for defining input scenarios, for setting system parameters and for initializing other experimental options must be selected in an efficient way. The use of computer algorithms to support experimental design in complex problems has been a topic of recent research in the areas of statistics and engineering. This paper describes a resampling based approach to form dating this design. An example is provided illustrating in two dimensions how the algorithm works and indicating its potential on larger problems. The results show that the proposed approach has characteristics desirable of an algorithmic approach on the simple examples. Further experimentation is needed to evaluate its performance on larger problems.
Automated Approach to Very High-Order Aeroacoustic Computations. Revision
NASA Technical Reports Server (NTRS)
Dyson, Rodger W.; Goodrich, John W.
2001-01-01
Computational aeroacoustics requires efficient, high-resolution simulation tools. For smooth problems, this is best accomplished with very high-order in space and time methods on small stencils. However, the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewski recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that am located near wall boundaries. These procedures are used to develop automatically and to implement very high-order methods (> 15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.
A New Approach on Computing Free Core Nutation
NASA Astrophysics Data System (ADS)
Zhang, Mian; Huang, Chengling
2015-04-01
Free core nutation (FCN) is a rotational modes of the earth related to non-alignment of the rotation axis of the core and of the mantle. FCN period by traditional theoretical methods is near 460 days with PREM, while the precise observations (VLBI + SG tides) say it should be near 430 days. In order to fill this big gap, astronomers and geophysicists give various assumptions, e.g., increasing core-mantle-boundary (CMB) flattening by about 5%, a strong coupling between nutation and geomagnetic field near CMB, viscous coupling, or topographical coupling etc. Do we really need these unproved assumptions? or is it only the problem of these traditional theoretical methods themselves? Earth models (e.g. PREM) provide accurate and robust profiles of physical parameters, like density and Lame parameters, but their radial derivatives, which are also used in all traditional methods to calculate normal modes (e.g.. FCN), nutation and tides of non-rigid earth theoretically, are not so trustable as the parameters themselves. A new stratified Galerkin method is proposed and applied to the computation of rotational modes, to avoid these problems. This new method can solve not only one order ellipsoid but also irregular asymmetric 3D earth model. Our primary result of the FCN period is 435 sidereal days.
Understanding auditory distance estimation by humpback whales: a computational approach.
Mercado, E; Green, S R; Schneider, J N
2008-02-01
Ranging, the ability to judge the distance to a sound source, depends on the presence of predictable patterns of attenuation. We measured long-range sound propagation in coastal waters to assess whether humpback whales might use frequency degradation cues to range singing whales. Two types of neural networks, a multi-layer and a single-layer perceptron, were trained to classify recorded sounds by distance traveled based on their frequency content. The multi-layer network successfully classified received sounds, demonstrating that the distorting effects of underwater propagation on frequency content provide sufficient cues to estimate source distance. Normalizing received sounds with respect to ambient noise levels increased the accuracy of distance estimates by single-layer perceptrons, indicating that familiarity with background noise can potentially improve a listening whale's ability to range. To assess whether frequency patterns predictive of source distance were likely to be perceived by whales, recordings were pre-processed using a computational model of the humpback whale's peripheral auditory system. Although signals processed with this model contained less information than the original recordings, neural networks trained with these physiologically based representations estimated source distance more accurately, suggesting that listening whales should be able to range singers using distance-dependent changes in frequency content.
A computational approach to studying ageing at the individual level
Mourão, Márcio A.; Schnell, Santiago; Pletcher, Scott D.
2016-01-01
The ageing process is actively regulated throughout an organism's life, but studying the rate of ageing in individuals is difficult with conventional methods. Consequently, ageing studies typically make biological inference based on population mortality rates, which often do not accurately reflect the probabilities of death at the individual level. To study the relationship between individual and population mortality rates, we integrated in vivo switch experiments with in silico stochastic simulations to elucidate how carefully designed experiments allow key aspects of individual ageing to be deduced from group mortality measurements. As our case study, we used the recent report demonstrating that pheromones of the opposite sex decrease lifespan in Drosophila melanogaster by reversibly increasing population mortality rates. We showed that the population mortality reversal following pheromone removal was almost surely occurring in individuals, albeit more slowly than suggested by population measures. Furthermore, heterogeneity among individuals due to the inherent stochasticity of behavioural interactions skewed population mortality rates in middle-age away from the individual-level trajectories of which they are comprised. This article exemplifies how computational models function as important predictive tools for designing wet-laboratory experiments to use population mortality rates to understand how genetic and environmental manipulations affect ageing in the individual. PMID:26865300
a Holistic Approach for Inspection of Civil Infrastructures Based on Computer Vision Techniques
NASA Astrophysics Data System (ADS)
Stentoumis, C.; Protopapadakis, E.; Doulamis, A.; Doulamis, N.
2016-06-01
In this work, it is examined the 2D recognition and 3D modelling of concrete tunnel cracks, through visual cues. At the time being, the structural integrity inspection of large-scale infrastructures is mainly performed through visual observations by human inspectors, who identify structural defects, rate them and, then, categorize their severity. The described approach targets at minimum human intervention, for autonomous inspection of civil infrastructures. The shortfalls of existing approaches in crack assessment are being addressed by proposing a novel detection scheme. Although efforts have been made in the field, synergies among proposed techniques are still missing. The holistic approach of this paper exploits the state of the art techniques of pattern recognition and stereo-matching, in order to build accurate 3D crack models. The innovation lies in the hybrid approach for the CNN detector initialization, and the use of the modified census transformation for stereo matching along with a binary fusion of two state-of-the-art optimization schemes. The described approach manages to deal with images of harsh radiometry, along with severe radiometric differences in the stereo pair. The effectiveness of this workflow is evaluated on a real dataset gathered in highway and railway tunnels. What is promising is that the computer vision workflow described in this work can be transferred, with adaptations of course, to other infrastructure such as pipelines, bridges and large industrial facilities that are in the need of continuous state assessment during their operational life cycle.
Ida, Masato; Taniguchi, Nobuyuki
2003-09-01
This paper introduces a candidate for the origin of the numerical instabilities in large eddy simulation repeatedly observed in academic and practical industrial flow computations. Without resorting to any subgrid-scale modeling, but based on a simple assumption regarding the streamwise component of flow velocity, it is shown theoretically that in a channel-flow computation, the application of the Gaussian filtering to the incompressible Navier-Stokes equations yields a numerically unstable term, a cross-derivative term, which is similar to one appearing in the Gaussian filtered Vlasov equation derived by Klimas [J. Comput. Phys. 68, 202 (1987)] and also to one derived recently by Kobayashi and Shimomura [Phys. Fluids 15, L29 (2003)] from the tensor-diffusivity subgrid-scale term in a dynamic mixed model. The present result predicts that not only the numerical methods and the subgrid-scale models employed but also only the applied filtering process can be a seed of this numerical instability. An investigation concerning the relationship between the turbulent energy scattering and the unstable term shows that the instability of the term does not necessarily represent the backscatter of kinetic energy which has been considered a possible origin of numerical instabilities in large eddy simulation. The present findings raise the question whether a numerically stable subgrid-scale model can be ideally accurate.
Computational Approaches for Microalgal Biofuel Optimization: A Review
Chaiboonchoe, Amphun
2014-01-01
The increased demand and consumption of fossil fuels have raised interest in finding renewable energy sources throughout the globe. Much focus has been placed on optimizing microorganisms and primarily microalgae, to efficiently produce compounds that can substitute for fossil fuels. However, the path to achieving economic feasibility is likely to require strain optimization through using available tools and technologies in the fields of systems and synthetic biology. Such approaches invoke a deep understanding of the metabolic networks of the organisms and their genomic and proteomic profiles. The advent of next generation sequencing and other high throughput methods has led to a major increase in availability of biological data. Integration of such disparate data can help define the emergent metabolic system properties, which is of crucial importance in addressing biofuel production optimization. Herein, we review major computational tools and approaches developed and used in order to potentially identify target genes, pathways, and reactions of particular interest to biofuel production in algae. As the use of these tools and approaches has not been fully implemented in algal biofuel research, the aim of this review is to highlight the potential utility of these resources toward their future implementation in algal research. PMID:25309916
Computational approaches for microalgal biofuel optimization: a review.
Koussa, Joseph; Chaiboonchoe, Amphun; Salehi-Ashtiani, Kourosh
2014-01-01
The increased demand and consumption of fossil fuels have raised interest in finding renewable energy sources throughout the globe. Much focus has been placed on optimizing microorganisms and primarily microalgae, to efficiently produce compounds that can substitute for fossil fuels. However, the path to achieving economic feasibility is likely to require strain optimization through using available tools and technologies in the fields of systems and synthetic biology. Such approaches invoke a deep understanding of the metabolic networks of the organisms and their genomic and proteomic profiles. The advent of next generation sequencing and other high throughput methods has led to a major increase in availability of biological data. Integration of such disparate data can help define the emergent metabolic system properties, which is of crucial importance in addressing biofuel production optimization. Herein, we review major computational tools and approaches developed and used in order to potentially identify target genes, pathways, and reactions of particular interest to biofuel production in algae. As the use of these tools and approaches has not been fully implemented in algal biofuel research, the aim of this review is to highlight the potential utility of these resources toward their future implementation in algal research.
Suggested Approaches to the Measurement of Computer Anxiety.
ERIC Educational Resources Information Center
Toris, Carol
Psychologists can gain insight into human behavior by examining what people feel about, know about, and do with, computers. Two extreme reactions to computers are computer phobia, or anxiety, and computer addiction, or "hacking". A four-part questionnaire was developed to measure computer anxiety. The first part is a projective technique which…
Computer Modeling of Violent Intent: A Content Analysis Approach
Sanfilippo, Antonio P.; Mcgrath, Liam R.; Bell, Eric B.
2014-01-03
We present a computational approach to modeling the intent of a communication source representing a group or an individual to engage in violent behavior. Our aim is to identify and rank aspects of radical rhetoric that are endogenously related to violent intent to predict the potential for violence as encoded in written or spoken language. We use correlations between contentious rhetoric and the propensity for violent behavior found in documents from radical terrorist and non-terrorist groups and individuals to train and evaluate models of violent intent. We then apply these models to unseen instances of linguistic behavior to detect signs of contention that have a positive correlation with violent intent factors. Of particular interest is the application of violent intent models to social media, such as Twitter, that have proved to serve as effective channels in furthering sociopolitical change.
Systems approaches to computational modeling of the oral microbiome
Dimitrov, Dimiter V.
2013-01-01
Current microbiome research has generated tremendous amounts of data providing snapshots of molecular activity in a variety of organisms, environments, and cell types. However, turning this knowledge into whole system level of understanding on pathways and processes has proven to be a challenging task. In this review we highlight the applicability of bioinformatics and visualization techniques to large collections of data in order to better understand the information that contains related diet—oral microbiome—host mucosal transcriptome interactions. In particular, we focus on systems biology of Porphyromonas gingivalis in the context of high throughput computational methods tightly integrated with translational systems medicine. Those approaches have applications for both basic research, where we can direct specific laboratory experiments in model organisms and cell cultures, and human disease, where we can validate new mechanisms and biomarkers for prevention and treatment of chronic disorders. PMID:23847548
Computational approaches to substrate-based cell motility
NASA Astrophysics Data System (ADS)
Ziebert, Falko; Aranson, Igor S.
2016-07-01
Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realisation of active, self-propelled 'particles', a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recently in its modelling on the whole-cell level. Here we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organised systems such as living cells.
Local-basis-function approach to computed tomography
NASA Astrophysics Data System (ADS)
Hanson, K. M.; Wecksung, G. W.
1985-12-01
In the local basis-function approach, a reconstruction is represented as a linear expansion of basis functions, which are arranged on a rectangular grid and possess a local region of support. The basis functions considered here are positive and may overlap. It is found that basis functions based on cubic B-splines offer significant improvements in the calculational accuracy that can be achieved with iterative tomographic reconstruction algorithms. By employing repetitive basis functions, the computational effort involved in these algorithms can be minimized through the use of tabulated values for the line or strip integrals over a single-basis function. The local nature of the basis functions reduces the difficulties associated with applying local constraints on reconstruction values, such as upper and lower limits. Since a reconstruction is specified everywhere by a set of coefficients, display of a coarsely represented image does not require an arbitrary choice of an interpolation function.
Computational Diagnostic: A Novel Approach to View Medical Data.
Mane, K. K.; Börner, K.
2007-01-01
A transition from traditional paper-based medical records to electronic health record is largely underway. The use of electronic records offers tremendous potential to personalize patient diagnosis and treatment. In this paper, we discuss a computational diagnostic tool that uses digital medical records to help doctors gain better insight about a patient's medical condition. The paper details different interactive features of the tool which offer potential to practice evidence-based medicine and advance patient diagnosis practices. The healthcare industry is a constantly evolving domain. Research from this domain is often translated into better understanding of different medical conditions. This new knowledge often contributes towards improved diagnosis and treatment solutions for patients. But the healthcare industry lags behind to seek immediate benefits of the new knowledge as it still adheres to the traditional paper-based approach to keep track of medical records. However recently we notice a drive that promotes a transition towards electronic health record (EHR). An EHR stores patient medical records in digital format and offers potential to replace the paper health records. Earlier attempts of an EHR replicated the paper layout on the screen, representation of medical history of a patient in a graphical time-series format, interactive visualization with 2D/3D generated images from an imaging device. But an EHR can be much more than just an 'electronic view' of the paper record or a collection of images from an imaging device. In this paper, we present an EHR called 'Computational Diagnostic Tool', that provides a novel computational approach to look at patient medical data. The developed EHR system is knowledge driven and acts as clinical decision support tool. The EHR tool provides two visual views of the medical data. Dynamic interaction with data is supported to help doctors practice evidence-based decisions and make judicious choices about patient
Palmquist, Anders; Shah, Furqan A; Emanuelsson, Lena; Omar, Omar; Suska, Felicia
2017-03-01
This paper investigates the application of X-ray micro-computed tomography (micro-CT) to accurately evaluate bone formation within 3D printed, porous Ti6Al4V implants manufactured using Electron Beam Melting (EBM), retrieved after six months of healing in sheep femur and tibia. All samples were scanned twice (i.e., before and after resin embedding), using fast, low-resolution scans (Skyscan 1172; Bruker micro-CT, Kontich, Belgium), and were analysed by 2D and 3D morphometry. The main questions posed were: (i) Can low resolution, fast scans provide morphometric data of bone formed inside (and around) metal implants with a complex, open-pore architecture?, (ii) Can micro-CT be used to accurately quantify both the bone area (BA) and bone-implant contact (BIC)?, (iii) What degree of error is introduced in the quantitative data by varying the threshold values?, and (iv) Does resin embedding influence the accuracy of the analysis? To validate the accuracy of micro-CT measurements, each data set was correlated with a corresponding centrally cut histological section. The results show that quantitative histomorphometry corresponds strongly with 3D measurements made by micro-CT, where a high correlation exists between the two techniques for bone area/volume measurements around and inside the porous network. On the contrary, the direct bone-implant contact is challenging to estimate accurately or reproducibly. Large errors may be introduced in micro-CT measurements when segmentation is performed without calibrating the data set against a corresponding histological section. Generally, the bone area measurement is strongly influenced by the lower threshold limit, while the upper threshold limit has little or no effect. Resin embedding does not compromise the accuracy of micro-CT measurements, although there is a change in the contrast distributions and optimisation of the threshold ranges is required.
Itu, Lucian; Rapaka, Saikiran; Passerini, Tiziano; Georgescu, Bogdan; Schwemmer, Chris; Schoebinger, Max; Flohr, Thomas; Sharma, Puneet; Comaniciu, Dorin
2016-07-01
Fractional flow reserve (FFR) is a functional index quantifying the severity of coronary artery lesions and is clinically obtained using an invasive, catheter-based measurement. Recently, physics-based models have shown great promise in being able to noninvasively estimate FFR from patient-specific anatomical information, e.g., obtained from computed tomography scans of the heart and the coronary arteries. However, these models have high computational demand, limiting their clinical adoption. In this paper, we present a machine-learning-based model for predicting FFR as an alternative to physics-based approaches. The model is trained on a large database of synthetically generated coronary anatomies, where the target values are computed using the physics-based model. The trained model predicts FFR at each point along the centerline of the coronary tree, and its performance was assessed by comparing the predictions against physics-based computations and against invasively measured FFR for 87 patients and 125 lesions in total. Correlation between machine-learning and physics-based predictions was excellent (0.9994, P < 0.001), and no systematic bias was found in Bland-Altman analysis: mean difference was -0.00081 ± 0.0039. Invasive FFR ≤ 0.80 was found in 38 lesions out of 125 and was predicted by the machine-learning algorithm with a sensitivity of 81.6%, a specificity of 83.9%, and an accuracy of 83.2%. The correlation was 0.729 (P < 0.001). Compared with the physics-based computation, average execution time was reduced by more than 80 times, leading to near real-time assessment of FFR. Average execution time went down from 196.3 ± 78.5 s for the CFD model to ∼2.4 ± 0.44 s for the machine-learning model on a workstation with 3.4-GHz Intel i7 8-core processor.
A T Borojeni, Azadeh; Frank-Ito, Dennis O; Kimbell, Julia S; Rhee, John S; Garcia, Guilherme J M
2016-08-15
Virtual surgery planning based on computational fluid dynamics (CFD) simulations has the potential to improve surgical outcomes for nasal airway obstruction patients, but the benefits of virtual surgery planning must outweigh the risks of radiation exposure. Cone beam computed tomography (CT) scans represent an attractive imaging modality for virtual surgery planning due to lower costs and lower radiation exposures compared with conventional CT scans. However, to minimize the radiation exposure, the cone beam CT sinusitis protocol sometimes images only the nasal cavity, excluding the nasopharynx. The goal of this study was to develop an idealized nasopharynx geometry for accurate representation of outlet boundary conditions when the nasopharynx geometry is unavailable. Anatomically accurate models of the nasopharynx created from 30 CT scans were intersected with planes rotated at different angles to obtain an average geometry. Cross sections of the idealized nasopharynx were approximated as ellipses with cross-sectional areas and aspect ratios equal to the average in the actual patient-specific models. CFD simulations were performed to investigate whether nasal airflow patterns were affected when the CT-based nasopharynx was replaced by the idealized nasopharynx in 10 nasal airway obstruction patients. Despite the simple form of the idealized geometry, all biophysical variables (nasal resistance, airflow rate, and heat fluxes) were very similar in the idealized vs patient-specific models. The results confirmed the expectation that the nasopharynx geometry has a minimal effect in the nasal airflow patterns during inspiration. The idealized nasopharynx geometry will be useful in future CFD studies of nasal airflow based on medical images that exclude the nasopharynx.
Examples of computational approaches for elliptic, possibly multiscale PDEs with random inputs
NASA Astrophysics Data System (ADS)
Le Bris, Claude; Legoll, Frédéric
2017-01-01
We overview a series of recent works addressing numerical simulations of partial differential equations in the presence of some elements of randomness. The specific equations manipulated are linear elliptic, and arise in the context of multiscale problems, but the purpose is more general. On a set of prototypical situations, we investigate two critical issues present in many settings: variance reduction techniques to obtain sufficiently accurate results at a limited computational cost when solving PDEs with random coefficients, and finite element techniques that are sufficiently flexible to carry over to geometries with random fluctuations. Some elements of theoretical analysis and numerical analysis are briefly mentioned. Numerical experiments, although simple, provide convincing evidence of the efficiency of the approaches.
NASA Astrophysics Data System (ADS)
Lebiedz, D.
2004-04-01
Advanced experimental techniques in chemistry and physics provide increasing access to detailed deterministic mass action models for chemical reaction kinetics. Especially in complex technical or biochemical systems the huge amount of species and reaction pathways involved in a detailed modeling approach call for efficient methods of model reduction. These should be automatic and based on a firm mathematical analysis of the ordinary differential equations underlying the chemical kinetics in deterministic models. A main purpose of model reduction is to enable accurate numerical simulations of even high dimensional and spatially extended reaction systems. The latter include physical transport mechanisms and are modeled by partial differential equations. Their numerical solution for hundreds or thousands of species within a reasonable time will exceed computer capacities available now and in a foreseeable future. The central idea of model reduction is to replace the high dimensional dynamics by a low dimensional approximation with an appropriate degree of accuracy. Here I present a global approach to model reduction based on the concept of minimal entropy production and its numerical implementation. For given values of a single species concentration in a chemical system all other species concentrations are computed under the assumption that the system is as close as possible to its attractor, the thermodynamic equilibrium, in the sense that all modes of thermodynamic forces are maximally relaxed except the one, which drives the remaining system dynamics. This relaxation is expressed in terms of minimal entropy production for single reaction steps along phase space trajectories.
González-Pérez, Pedro P; Orta, Daniel J; Peña, Irving; Flores, Eduardo C; Ramírez, José U; Beltrán, Hiram I; Alas, Salomón J
2017-02-08
Intracellular protein folding (PF) is performed in a highly inhomogeneous, crowded, and correlated environment. Due to this inherent complexity, the study and understanding of PF phenomena is a fundamental issue in the field of computational systems biology. In particular, it is important to use a modeled medium that accurately reflects PF in natural systems. In the current study, we present a simulation wherein PF is carried out within an inhomogeneous modeled medium. Simulation resources included a two-dimensional hydrophobic-polar (HP) model, evolutionary algorithms, and the dual site-bond model. The dual site-bond model was used to develop an environment where HP beads could be folded. Our modeled medium included correlation lengths and fractal-like behavior, which were selected according to HP sequence lengths to induce folding in a crowded environment. Analysis of three benchmark HP sequences showed that the modeled inhomogeneous space played an important role in deeper energy folding and obtained better performance and convergence compared with homogeneous environments. Our computational approach also demonstrated that our correlated network provided a better space for PF. Thus, our approach represents a major advancement in PF simulations, not only for folding but also for understanding functional chemical structure and physicochemical properties of proteins in crowded molecular systems, which normally occur in nature.
NASA Astrophysics Data System (ADS)
Kiese, Sandra; Kücükpinar, Esra; Reinelt, Matthias; Miesbauer, Oliver; Ewender, Johann; Langowski, Horst-Christian
2017-02-01
Flexible organic electronic devices are often protected from degradation by encapsulation in multilayered films with very high barrier properties against moisture and oxygen. However, metrology must be improved to detect such low quantities of permeants. We therefore developed a modified ultra-low permeation measurement device based on a constant-flow carrier-gas system to measure both the transient and stationary water vapor permeation through high-performance barrier films. The accumulation of permeated water vapor before its transport to the detector allows the measurement of very low water vapor transmission rates (WVTRs) down to 2 × 10-5 g m-2 d-1. The measurement cells are stored in a temperature-controlled chamber, allowing WVTR measurements within the temperature range 23-80 °C. Differences in relative humidity can be controlled within the range 15%-90%. The WVTR values determined using the novel measurement device agree with those measured using a commercially available carrier-gas device from MOCON®. Depending on the structure and quality of the barrier film, it may take a long time for the WVTR to reach a steady-state value. However, by using a combination of the time-dependent measurement and the finite element method, we were able to estimate the steady-state WVTR accurately with significantly shorter measurement times.
An Evolutionary Computation Approach to Examine Functional Brain Plasticity
Roy, Arnab; Campbell, Colin; Bernier, Rachel A.; Hillary, Frank G.
2016-01-01
One common research goal in systems neurosciences is to understand how the functional relationship between a pair of regions of interest (ROIs) evolves over time. Examining neural connectivity in this way is well-suited for the study of developmental processes, learning, and even in recovery or treatment designs in response to injury. For most fMRI based studies, the strength of the functional relationship between two ROIs is defined as the correlation between the average signal representing each region. The drawback to this approach is that much information is lost due to averaging heterogeneous voxels, and therefore, the functional relationship between a ROI-pair that evolve at a spatial scale much finer than the ROIs remain undetected. To address this shortcoming, we introduce a novel evolutionary computation (EC) based voxel-level procedure to examine functional plasticity between an investigator defined ROI-pair by simultaneously using subject-specific BOLD-fMRI data collected from two sessions seperated by finite duration of time. This data-driven procedure detects a sub-region composed of spatially connected voxels from each ROI (a so-called sub-regional-pair) such that the pair shows a significant gain/loss of functional relationship strength across the two time points. The procedure is recursive and iteratively finds all statistically significant sub-regional-pairs within the ROIs. Using this approach, we examine functional plasticity between the default mode network (DMN) and the executive control network (ECN) during recovery from traumatic brain injury (TBI); the study includes 14 TBI and 12 healthy control subjects. We demonstrate that the EC based procedure is able to detect functional plasticity where a traditional averaging based approach fails. The subject-specific plasticity estimates obtained using the EC-procedure are highly consistent across multiple runs. Group-level analyses using these plasticity estimates showed an increase in the strength
Brounstein, Anna; Hacihaliloglu, Ilker; Guy, Pierre; Hodgson, Antony; Abugharbieh, Rafeef
2015-12-01
Automatic, accurate and real-time registration is an important step in providing effective guidance and successful anatomic restoration in ultrasound (US)-based computer assisted orthopedic surgery. We propose a method in which local phase-based bone surfaces, extracted from intra-operative US data, are registered to pre-operatively segmented computed tomography data. Extracted bone surfaces are downsampled and reinforced with high curvature features. A novel hierarchical simplification algorithm is used to further optimize the point clouds. The final point clouds are represented as Gaussian mixture models and iteratively matched by minimizing the dissimilarity between them using an L2 metric. For 44 clinical data sets from 25 pelvic fracture patients and 49 phantom data sets, we report mean surface registration accuracies of 0.31 and 0.77 mm, respectively, with an average registration time of 1.41 s. Our results suggest the viability and potential of the chosen method for real-time intra-operative registration in orthopedic surgery.
Krishna Kumar, P; Araki, Tadashi; Rajan, Jeny; Saba, Luca; Lavra, Francesco; Ikeda, Nobutaka; Sharma, Aditya M; Shafique, Shoaib; Nicolaides, Andrew; Laird, John R; Gupta, Ajay; Suri, Jasjit S
2016-12-10
Monitoring of cerebrovascular diseases via carotid ultrasound has started to become a routine. The measurement of image-based lumen diameter (LD) or inter-adventitial diameter (IAD) is a promising approach for quantification of the degree of stenosis. The manual measurements of LD/IAD are not reliable, subjective and slow. The curvature associated with the vessels along with non-uniformity in the plaque growth poses further challenges. This study uses a novel and generalized approach for automated LD and IAD measurement based on a combination of spatial transformation and scale-space. In this iterative procedure, the scale-space is first used to get the lumen axis which is then used with spatial image transformation paradigm to get a transformed image. The scale-space is then reapplied to retrieve the lumen region and boundary in the transformed framework. Then, inverse transformation is applied to display the results in original image framework. Two hundred and two patients' left and right common carotid artery (404 carotid images) B-mode ultrasound images were retrospectively analyzed. The validation of our algorithm has done against the two manual expert tracings. The coefficient of correlation between the two manual tracings for LD was 0.98 (p < 0.0001) and 0.99 (p < 0.0001), respectively. The precision of merit between the manual expert tracings and the automated system was 97.7 and 98.7%, respectively. The experimental analysis demonstrated superior performance of the proposed method over conventional approaches. Several statistical tests demonstrated the stability and reliability of the automated system.
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects.
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861
NASA Astrophysics Data System (ADS)
Ihrig, Arvid Conrad; Wieferink, Jürgen; Zhang, Igor Ying; Ropo, Matti; Ren, Xinguo; Rinke, Patrick; Scheffler, Matthias; Blum, Volker
2015-09-01
A key component in calculations of exchange and correlation energies is the Coulomb operator, which requires the evaluation of two-electron integrals. For localized basis sets, these four-center integrals are most efficiently evaluated with the resolution of identity (RI) technique, which expands basis-function products in an auxiliary basis. In this work we show the practical applicability of a localized RI-variant (‘RI-LVL’), which expands products of basis functions only in the subset of those auxiliary basis functions which are located at the same atoms as the basis functions. We demonstrate the accuracy of RI-LVL for Hartree-Fock calculations, for the PBE0 hybrid density functional, as well as for RPA and MP2 perturbation theory. Molecular test sets used include the S22 set of weakly interacting molecules, the G3 test set, as well as the G2-1 and BH76 test sets, and heavy elements including titanium dioxide, copper and gold clusters. Our RI-LVL implementation paves the way for linear-scaling RI-based hybrid functional calculations for large systems and for all-electron many-body perturbation theory with significantly reduced computational and memory cost.
A systems approach to computer-based training
NASA Technical Reports Server (NTRS)
Drape, Gaylen W.
1994-01-01
This paper describes the hardware and software systems approach used in the Automated Recertification Training System (ARTS), a Phase 2 Small Business Innovation Research (SBIR) project for NASA Kennedy Space Center (KSC). The goal of this project is to optimize recertification training of technicians who process the Space Shuttle before launch by providing computer-based training courseware. The objectives of ARTS are to implement more effective CBT applications identified through a need assessment process and to provide an ehanced courseware production system. The system's capabilities are demonstrated by using five different pilot applications to convert existing classroom courses into interactive courseware. When the system is fully implemented at NASA/KSC, trainee job performance will improve and the cost of courseware development will be lower. Commercialization of the technology developed as part of this SBIR project is planned for Phase 3. Anticipated spin-off products include custom courseware for technical skills training and courseware production software for use by corporate training organizations of aerospace and other industrial companies.
Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection
Ding, Hong; Dwaraknath, Shyam S.; Garten, Lauren; Ndione, Paul; Ginley, David; Persson, Kristin A.
2016-05-25
With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO2 compounds which provides a rich chemical and structural polymorph space. We find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO2 substrates, where the VO2 brookite phase would be preferentially grown on the a-c TiO2 brookite plane while the columbite and anatase structures favor the a-b plane on the respective TiO2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. These criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available.
Computer-aided interpretation approach for optical tomographic images
NASA Astrophysics Data System (ADS)
Klose, Christian D.; Klose, Alexander D.; Netz, Uwe J.; Scheel, Alexander K.; Beuthan, Jürgen; Hielscher, Andreas H.
2010-11-01
A computer-aided interpretation approach is proposed to detect rheumatic arthritis (RA) in human finger joints using optical tomographic images. The image interpretation method employs a classification algorithm that makes use of a so-called self-organizing mapping scheme to classify fingers as either affected or unaffected by RA. Unlike in previous studies, this allows for combining multiple image features, such as minimum and maximum values of the absorption coefficient for identifying affected and not affected joints. Classification performances obtained by the proposed method were evaluated in terms of sensitivity, specificity, Youden index, and mutual information. Different methods (i.e., clinical diagnostics, ultrasound imaging, magnet resonance imaging, and inspection of optical tomographic images), were used to produce ground truth benchmarks to determine the performance of image interpretations. Using data from 100 finger joints, findings suggest that some parameter combinations lead to higher sensitivities, while others to higher specificities when compared to single parameter classifications employed in previous studies. Maximum performances are reached when combining the minimum/maximum ratio of the absorption coefficient and image variance. In this case, sensitivities and specificities over 0.9 can be achieved. These values are much higher than values obtained when only single parameter classifications were used, where sensitivities and specificities remained well below 0.8.
A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors
Gayvert, Kaitlyn; Dardenne, Etienne; Cheung, Cynthia; Boland, Mary Regina; Lorberbaum, Tal; Wanjala, Jackline; Chen, Yu; Rubin, Mark; Tatonetti, Nicholas P.; Rickman, David; Elemento, Olivier
2016-01-01
Summary Mutations in transcription factors (TFs) genes are frequently observed in tumors, often leading to aberrant transcriptional activity. Unfortunately, TFs are often considered undruggable due to the absence of targetable enzymatic activity. To address this problem, we developed CRAFTT, a Computational drug-Repositioning Approach For Targeting Transcription factor activity. CRAFTT combines ChIP-seq with drug-induced expression profiling to identify small molecules that can specifically perturb TF activity. Application to ENCODE ChIP-seq datasets revealed known drug-TF interactions and a global drug-protein network analysis further supported these predictions. Application of CRAFTT to ERG, a pro-invasive, frequently over-expressed oncogenic TF predicted that dexamethasone would inhibit ERG activity. Indeed, dexamethasone significantly decreased cell invasion and migration in an ERG-dependent manner. Furthermore, analysis of Electronic Medical Record data indicates a protective role for dexamethasone against prostate cancer. Altogether, our method provides a broadly applicable strategy to identify drugs that specifically modulate TF activity. PMID:27264179
An Integrated Soft Computing Approach to Hughes Syndrome Risk Assessment.
Vilhena, João; Rosário Martins, M; Vicente, Henrique; Grañeda, José M; Caldeira, Filomena; Gusmão, Rodrigo; Neves, João; Neves, José
2017-03-01
The AntiPhospholipid Syndrome (APS) is an acquired autoimmune disorder induced by high levels of antiphospholipid antibodies that cause arterial and veins thrombosis, as well as pregnancy-related complications and morbidity, as clinical manifestations. This autoimmune hypercoagulable state, usually known as Hughes syndrome, has severe consequences for the patients, being one of the main causes of thrombotic disorders and death. Therefore, it is required to be preventive; being aware of how probable is to have that kind of syndrome. Despite the updated of antiphospholipid syndrome classification, the diagnosis remains difficult to establish. Additional research on clinically relevant antibodies and standardization of their quantification are required in order to improve the antiphospholipid syndrome risk assessment. Thus, this work will focus on the development of a diagnosis decision support system in terms of a formal agenda built on a Logic Programming approach to knowledge representation and reasoning, complemented with a computational framework based on Artificial Neural Networks. The proposed model allows for improving the diagnosis, classifying properly the patients that really presented this pathology (sensitivity higher than 85%), as well as classifying the absence of APS (specificity close to 95%).
Computer-aided interpretation approach for optical tomographic images.
Klose, Christian D; Klose, Alexander D; Netz, Uwe J; Scheel, Alexander K; Beuthan, Jurgen; Hielscher, Andreas H
2010-01-01
A computer-aided interpretation approach is proposed to detect rheumatic arthritis (RA) in human finger joints using optical tomographic images. The image interpretation method employs a classification algorithm that makes use of a so-called self-organizing mapping scheme to classify fingers as either affected or unaffected by RA. Unlike in previous studies, this allows for combining multiple image features, such as minimum and maximum values of the absorption coefficient for identifying affected and not affected joints. Classification performances obtained by the proposed method were evaluated in terms of sensitivity, specificity, Youden index, and mutual information. Different methods (i.e., clinical diagnostics, ultrasound imaging, magnet resonance imaging, and inspection of optical tomographic images), were used to produce ground truth benchmarks to determine the performance of image interpretations. Using data from 100 finger joints, findings suggest that some parameter combinations lead to higher sensitivities, while others to higher specificities when compared to single parameter classifications employed in previous studies. Maximum performances are reached when combining the minimum/maximum ratio of the absorption coefficient and image variance. In this case, sensitivities and specificities over 0.9 can be achieved. These values are much higher than values obtained when only single parameter classifications were used, where sensitivities and specificities remained well below 0.8.
Lexical is as lexical does: computational approaches to lexical representation
Woollams, Anna M.
2015-01-01
In much of neuroimaging and neuropsychology, regions of the brain have been associated with ‘lexical representation’, with little consideration as to what this cognitive construct actually denotes. Within current computational models of word recognition, there are a number of different approaches to the representation of lexical knowledge. Structural lexical representations, found in original theories of word recognition, have been instantiated in modern localist models. However, such a representational scheme lacks neural plausibility in terms of economy and flexibility. Connectionist models have therefore adopted distributed representations of form and meaning. Semantic representations in connectionist models necessarily encode lexical knowledge. Yet when equipped with recurrent connections, connectionist models can also develop attractors for familiar forms that function as lexical representations. Current behavioural, neuropsychological and neuroimaging evidence shows a clear role for semantic information, but also suggests some modality- and task-specific lexical representations. A variety of connectionist architectures could implement these distributed functional representations, and further experimental and simulation work is required to discriminate between these alternatives. Future conceptualisations of lexical representations will therefore emerge from a synergy between modelling and neuroscience. PMID:25893204
NASA Astrophysics Data System (ADS)
Neese, Frank; Wennmohs, Frank; Hansen, Andreas
2009-03-01
Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500
De Backer, A; van den Bos, K H W; Van den Broek, W; Sijbers, J; Van Aert, S
2016-12-01
An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
An Educational Approach to Computationally Modeling Dynamical Systems
ERIC Educational Resources Information Center
Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl
2009-01-01
Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…
Computational approaches to stochastic systems in physics and biology
NASA Astrophysics Data System (ADS)
Jeraldo Maldonado, Patricio Rodrigo
In this dissertation, I devise computational approaches to model and understand two very different systems which exhibit stochastic behavior: quantum fluids with topological defects arising during quenches and forcing, and complex microbial communities living and evolving with the gastrointestinal tracts of vertebrates. As such, this dissertation is organized into two parts. In Part I, I create a model for quantum fluids, which incorporates a conservative and dissipative part, and I also allow the fluid to be externally forced by a normal fluid. I use then this model to calculate scaling laws arising from the stochastic interactions of the topological defects exhibited by the modeled fluid while undergoing a quench. In Chapter 2 I give a detailed description of this model of quantum fluids. Unlike more traditional approaches, this model is based on Cell Dynamical Systems (CDS), an approach that captures relevant physical features of the system and allows for long time steps during its evolution. I devise a two step CDS model, implementing both conservative and dissipative dynamics present in quantum fluids. I also couple the model with an external normal fluid field that drives the system. I then validate the results of the model by measuring different scaling laws predicted for quantum fluids. I also propose an extension of the model that also incorporates the excitations of the fluid and couples its dynamics with the dynamics of the condensate. In Chapter 3 I use the above model to calculate scaling laws predicted for the velocity of topological defects undergoing a critical quench. To accomplish this, I numerically implement an algorithm that extracts from the order parameter field the velocity components of the defects as they move during the quench process. This algorithm is robust and extensible to any system where defects are located by the zeros of the order parameter. The algorithm is also applied to a sheared stripe-forming system, allowing the
NASA Astrophysics Data System (ADS)
Je, U. K.; Cho, H. M.; Cho, H. S.; Park, Y. O.; Park, C. K.; Lim, H. W.; Kim, K. S.; Kim, G. A.; Park, S. Y.; Woo, T. H.; Choi, S. I.
2016-02-01
In this paper, we propose a new/next-generation type of CT examinations, the so-called Interior Computed Tomography (ICT), which may presumably lead to dose reduction to the patient outside the target region-of-interest (ROI), in dental x-ray imaging. Here an x-ray beam from each projection position covers only a relatively small ROI containing a target of diagnosis from the examined structure, leading to imaging benefits such as decreasing scatters and system cost as well as reducing imaging dose. We considered the compressed-sensing (CS) framework, rather than common filtered-backprojection (FBP)-based algorithms, for more accurate ICT reconstruction. We implemented a CS-based ICT algorithm and performed a systematic simulation to investigate the imaging characteristics. Simulation conditions of two ROI ratios of 0.28 and 0.14 between the target and the whole phantom sizes and four projection numbers of 360, 180, 90, and 45 were tested. We successfully reconstructed ICT images of substantially high image quality by using the CS framework even with few-view projection data, still preserving sharp edges in the images.
Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M
2016-12-08
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
A computational intelligence approach to the Mars Precision Landing problem
NASA Astrophysics Data System (ADS)
Birge, Brian Kent, III
Various proposed Mars missions, such as the Mars Sample Return Mission (MRSR) and the Mars Smart Lander (MSL), require precise re-entry terminal position and velocity states. This is to achieve mission objectives including rendezvous with a previous landed mission, or reaching a particular geographic landmark. The current state of the art footprint is in the magnitude of kilometers. For this research a Mars Precision Landing is achieved with a landed footprint of no more than 100 meters, for a set of initial entry conditions representing worst guess dispersions. Obstacles to reducing the landed footprint include trajectory dispersions due to initial atmospheric entry conditions (entry angle, parachute deployment height, etc.), environment (wind, atmospheric density, etc.), parachute deployment dynamics, unavoidable injection error (propagated error from launch on), etc. Weather and atmospheric models have been developed. Three descent scenarios have been examined. First, terminal re-entry is achieved via a ballistic parachute with concurrent thrusting events while on the parachute, followed by a gravity turn. Second, terminal re-entry is achieved via a ballistic parachute followed by gravity turn to hover and then thrust vector to desired location. Third, a guided parafoil approach followed by vectored thrusting to reach terminal velocity is examined. The guided parafoil is determined to be the best architecture. The purpose of this study is to examine the feasibility of using a computational intelligence strategy to facilitate precision planetary re-entry, specifically to take an approach that is somewhat more intuitive and less rigid, and see where it leads. The test problems used for all research are variations on proposed Mars landing mission scenarios developed by NASA. A relatively recent method of evolutionary computation is Particle Swarm Optimization (PSO), which can be considered to be in the same general class as Genetic Algorithms. An improvement over
A Soft Computing Approach to Kidney Diseases Evaluation.
Neves, José; Martins, M Rosário; Vilhena, João; Neves, João; Gomes, Sabino; Abelha, António; Machado, José; Vicente, Henrique
2015-10-01
Kidney renal failure means that one's kidney have unexpectedly stopped functioning, i.e., once chronic disease is exposed, the presence or degree of kidney dysfunction and its progression must be assessed, and the underlying syndrome has to be diagnosed. Although the patient's history and physical examination may denote good practice, some key information has to be obtained from valuation of the glomerular filtration rate, and the analysis of serum biomarkers. Indeed, chronic kidney sickness depicts anomalous kidney function and/or its makeup, i.e., there is evidence that treatment may avoid or delay its progression, either by reducing and prevent the development of some associated complications, namely hypertension, obesity, diabetes mellitus, and cardiovascular complications. Acute kidney injury appears abruptly, with a rapid deterioration of the renal function, but is often reversible if it is recognized early and treated promptly. In both situations, i.e., acute kidney injury and chronic kidney disease, an early intervention can significantly improve the prognosis. The assessment of these pathologies is therefore mandatory, although it is hard to do it with traditional methodologies and existing tools for problem solving. Hence, in this work, we will focus on the development of a hybrid decision support system, in terms of its knowledge representation and reasoning procedures based on Logic Programming, that will allow one to consider incomplete, unknown, and even contradictory information, complemented with an approach to computing centered on Artificial Neural Networks, in order to weigh the Degree-of-Confidence that one has on such a happening. The present study involved 558 patients with an age average of 51.7 years and the chronic kidney disease was observed in 175 cases. The dataset comprise twenty four variables, grouped into five main categories. The proposed model showed a good performance in the diagnosis of chronic kidney disease, since the
Gast, P; Mance, D; Zurlo, E; Ivanov, K L; Baldus, M; Huber, M
2017-02-01
To understand the dynamic nuclear polarization (DNP) enhancements of biradical polarizing agents, the magnetic resonance parameters need to be known. We describe a tailored EPR approach to accurately determine electron spin-spin coupling parameters using a combination of standard (9 GHz), high (95 GHz) and ultra-high (275 GHz) frequency EPR. Comparing liquid- and frozen-solution continuous-wave EPR spectra provides accurate anisotropic dipolar interaction D and isotropic exchange interaction J parameters of the DNP biradical AMUPol. We found that D was larger by as much as 30% compared to earlier estimates, and that J is 43 MHz, whereas before it was considered to be negligible. With the refined data, quantum mechanical calculations confirm that an increase in dipolar electron-electron couplings leads to higher cross-effect DNP efficiencies. Moreover, the DNP calculations qualitatively reproduce the difference of TOTAPOL and AMUPol DNP efficiencies found experimentally and suggest that AMUPol is particularly effective in improving the DNP efficiency at magnetic fields higher than 500 MHz. The multi-frequency EPR approach will aid in predicting the optimal structures for future DNP agents.
NASA Astrophysics Data System (ADS)
Rybynok, V. O.; Kyriacou, P. A.
2007-10-01
Diabetes is one of the biggest health challenges of the 21st century. The obesity epidemic, sedentary lifestyles and an ageing population mean prevalence of the condition is currently doubling every generation. Diabetes is associated with serious chronic ill health, disability and premature mortality. Long-term complications including heart disease, stroke, blindness, kidney disease and amputations, make the greatest contribution to the costs of diabetes care. Many of these long-term effects could be avoided with earlier, more effective monitoring and treatment. Currently, blood glucose can only be monitored through the use of invasive techniques. To date there is no widely accepted and readily available non-invasive monitoring technique to measure blood glucose despite the many attempts. This paper challenges one of the most difficult non-invasive monitoring techniques, that of blood glucose, and proposes a new novel approach that will enable the accurate, and calibration free estimation of glucose concentration in blood. This approach is based on spectroscopic techniques and a new adaptive modelling scheme. The theoretical implementation and the effectiveness of the adaptive modelling scheme for this application has been described and a detailed mathematical evaluation has been employed to prove that such a scheme has the capability of extracting accurately the concentration of glucose from a complex biological media.
Role of Soft Computing Approaches in HealthCare Domain: A Mini Review.
Gambhir, Shalini; Malik, Sanjay Kumar; Kumar, Yugal
2016-12-01
In the present era, soft computing approaches play a vital role in solving the different kinds of problems and provide promising solutions. Due to popularity of soft computing approaches, these approaches have also been applied in healthcare data for effectively diagnosing the diseases and obtaining better results in comparison to traditional approaches. Soft computing approaches have the ability to adapt itself according to problem domain. Another aspect is a good balance between exploration and exploitation processes. These aspects make soft computing approaches more powerful, reliable and efficient. The above mentioned characteristics make the soft computing approaches more suitable and competent for health care data. The first objective of this review paper is to identify the various soft computing approaches which are used for diagnosing and predicting the diseases. Second objective is to identify various diseases for which these approaches are applied. Third objective is to categories the soft computing approaches for clinical support system. In literature, it is found that large number of soft computing approaches have been applied for effectively diagnosing and predicting the diseases from healthcare data. Some of these are particle swarm optimization, genetic algorithm, artificial neural network, support vector machine etc. A detailed discussion on these approaches are presented in literature section. This work summarizes various soft computing approaches used in healthcare domain in last one decade. These approaches are categorized in five different categories based on the methodology, these are classification model based system, expert system, fuzzy and neuro fuzzy system, rule based system and case based system. Lot of techniques are discussed in above mentioned categories and all discussed techniques are summarized in the form of tables also. This work also focuses on accuracy rate of soft computing technique and tabular information is provided for
One of the strategic objectives of the Computational Toxicology Program is to develop approaches for prioritizing chemicals for subsequent screening and testing. Approaches currently available for this process require extensive resources. Therefore, less costly and time-extensi...
NASA Astrophysics Data System (ADS)
Riviere, Jim E.; Scoglio, Caterina; Sahneh, Faryad D.; Monteiro-Riviere, Nancy A.
2013-01-01
The field of nanomaterial pharmacokinetics is in its infancy, with major advances largely restricted by a lack of biologically relevant metrics, fundamental differences between particles and small molecules of organic chemicals and drugs relative to biological processes involved in disposition, a scarcity of sufficiently rich and characterized in vivo data and a lack of computational approaches to integrating nanomaterial properties to biological endpoints. A central concept that links nanomaterial properties to biological disposition, in addition to their colloidal properties, is the tendency to form a biocorona which modulates biological interactions including cellular uptake and biodistribution. Pharmacokinetic models must take this crucial process into consideration to accurately predict in vivo disposition, especially when extrapolating from laboratory animals to humans since allometric principles may not be applicable. The dynamics of corona formation, which modulates biological interactions including cellular uptake and biodistribution, is thereby a crucial process involved in the rate and extent of biodisposition. The challenge will be to develop a quantitative metric that characterizes a nanoparticle's surface adsorption forces that are important for predicting biocorona dynamics. These types of integrative quantitative approaches discussed in this paper for the dynamics of corona formation must be developed before realistic engineered nanomaterial risk assessment can be accomplished.
Discovery of novel hydrogen storage materials: an atomic scale computational approach.
Wolverton, C; Siegel, Donald J; Akbarzadeh, A R; Ozoliņš, V
2008-02-13
Practical hydrogen storage for mobile applications requires materials that exhibit high hydrogen densities, low decomposition temperatures, and fast kinetics for absorption and desorption. Unfortunately, no reversible materials are currently known that possess all of these attributes. Here we present an overview of our recent efforts aimed at developing a first-principles computational approach to the discovery of novel hydrogen storage materials. Such an approach requires several key capabilities to be effective: (i) accurate prediction of decomposition thermodynamics, (ii) prediction of crystal structures for unknown hydrides, and (iii) prediction of preferred decomposition pathways. We present examples that illustrate each of these three capabilities: (i) prediction of hydriding enthalpies and free energies across a wide range of hydride materials, (ii) prediction of low energy crystal structures for complex hydrides (such as Ca(AlH(4))(2) CaAlH(5), and Li(2)NH), and (iii) predicted decomposition pathways for Li(4)BN(3)H(10) and destabilized systems based on combinations of LiBH(4), Ca(BH(4))(2) and metal hydrides. For the destabilized systems, we propose a set of thermodynamic guidelines to help identify thermodynamically viable reactions. These capabilities have led to the prediction of several novel high density hydrogen storage materials and reactions.
Securing Applications in Personal Computers: The Relay Race Approach
1991-09-01
1987. Tanenbaum, A., Structured Computer Organizaticn, Prentice- Hall, Inc., 1990. Zarger, C., "Is Your PC Secure?" Mechanical Engineering, pg. 57...Operating Systems:Design and Implementation, Prentice-Hall, Inc., 1987. Tanenbaum, A., Structured Computer Organization, Prentice- Hall, Inc., 1990. Walker
An HCI Approach to Computing in the Real World
ERIC Educational Resources Information Center
Yardi, Sarita; Krolikowski, Pamela; Marshall, Taneshia; Bruckman, Amy
2008-01-01
We describe the implementation of a six-week course to teach Human-Computer Interaction (HCI) to high school students. Our goal was to explore the potential of HCI in motivating students to pursue future studies in related computing fields. Participants in our course learned to make connections between the types of technology they use in their…
The Computer Connection: Four Approaches to Microcomputer Laboratory Interfacing.
ERIC Educational Resources Information Center
Graef, Jean L.
1983-01-01
Four ways in which microcomputers can be turned into laboratory instruments are discussed. These include adding an analog/digital (A/D) converter on a printed circuit board, adding an external A/D converter using the computer's serial port, attaching transducers to the game paddle ports, or connecting an instrument to the computer. (JN)
Heinz, Hendrik
2014-06-18
Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.
Accurate Finite Difference Algorithms
NASA Technical Reports Server (NTRS)
Goodrich, John W.
1996-01-01
Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.
NASA Astrophysics Data System (ADS)
Gupta, Vipin; Kale, Amit; Sundar, Hari
2012-03-01
In this paper we propose a novel approach based on multi-stage random forests to address problems faced by traditional vessel segmentation algorithms on account of image artifacts such as stitches organ shadows etc.. Our approach consists of collecting a very large number of training data consisting of positive and negative examples of valid seed points. The method makes use of a 14x14 window around a putative seed point. For this window three types of feature vectors are computed viz. vesselness, eigenvalue and a novel effective margin feature. A random forest RF is trained for each of the feature vectors. At run time the three RFs are applied in succession to a putative seed point generated by a naiive vessel detection algorithm based on vesselness. Our approach will prune this set of putative seed points to correctly identify true seed points thereby avoiding false positives. We demonstrate the effectiveness of our algorithm on a large dataset of angio images.
Neutron stimulated emission computed tomography: a Monte Carlo simulation approach.
Sharma, A C; Harrawood, B P; Bender, J E; Tourassi, G D; Kapadia, A J
2007-10-21
A Monte Carlo simulation has been developed for neutron stimulated emission computed tomography (NSECT) using the GEANT4 toolkit. NSECT is a new approach to biomedical imaging that allows spectral analysis of the elements present within the sample. In NSECT, a beam of high-energy neutrons interrogates a sample and the nuclei in the sample are stimulated to an excited state by inelastic scattering of the neutrons. The characteristic gammas emitted by the excited nuclei are captured in a spectrometer to form multi-energy spectra. Currently, a tomographic image is formed using a collimated neutron beam to define the line integral paths for the tomographic projections. These projection data are reconstructed to form a representation of the distribution of individual elements in the sample. To facilitate the development of this technique, a Monte Carlo simulation model has been constructed from the GEANT4 toolkit. This simulation includes modeling of the neutron beam source and collimation, the samples, the neutron interactions within the samples, the emission of characteristic gammas, and the detection of these gammas in a Germanium crystal. In addition, the model allows the absorbed radiation dose to be calculated for internal components of the sample. NSECT presents challenges not typically addressed in Monte Carlo modeling of high-energy physics applications. In order to address issues critical to the clinical development of NSECT, this paper will describe the GEANT4 simulation environment and three separate simulations performed to accomplish three specific aims. First, comparison of a simulation to a tomographic experiment will verify the accuracy of both the gamma energy spectra produced and the positioning of the beam relative to the sample. Second, parametric analysis of simulations performed with different user-defined variables will determine the best way to effectively model low energy neutrons in tissue, which is a concern with the high hydrogen content in
Mapping Agricultural Fields in Sub-Saharan Africa with a Computer Vision Approach
NASA Astrophysics Data System (ADS)
Debats, S. R.; Luo, D.; Estes, L. D.; Fuchs, T.; Caylor, K. K.
2014-12-01
Sub-Saharan Africa is an important focus for food security research, because it is experiencing unprecedented population growth, agricultural activities are largely dominated by smallholder production, and the region is already home to 25% of the world's undernourished. One of the greatest challenges to monitoring and improving food security in this region is obtaining an accurate accounting of the spatial distribution of agriculture. Households are the primary units of agricultural production in smallholder communities and typically rely on small fields of less than 2 hectares. Field sizes are directly related to household crop productivity, management choices, and adoption of new technologies. As population and agriculture expand, it becomes increasingly important to understand both the distribution of field sizes as well as how agricultural communities are spatially embedded in the landscape. In addition, household surveys, a common tool for tracking agricultural productivity in Sub-Saharan Africa, would greatly benefit from spatially explicit accounting of fields. Current gridded land cover data sets do not provide information on individual agricultural fields or the distribution of field sizes. Therefore, we employ cutting edge approaches from the field of computer vision to map fields across Sub-Saharan Africa, including semantic segmentation, discriminative classifiers, and automatic feature selection. Our approach aims to not only improve the binary classification accuracy of cropland, but also to isolate distinct fields, thereby capturing crucial information on size and geometry. Our research focuses on the development of descriptive features across scales to increase the accuracy and geographic range of our computer vision algorithm. Relevant data sets include high-resolution remote sensing imagery and Landsat (30-m) multi-spectral imagery. Training data for field boundaries is derived from hand-digitized data sets as well as crowdsourcing.
Modeling weakly-ionized plasmas in magnetic field: A new computationally-efficient approach
Parent, Bernard; Macheret, Sergey O.; Shneider, Mikhail N.
2015-11-01
Despite its success at simulating accurately both non-neutral and quasi-neutral weakly-ionized plasmas, the drift-diffusion model has been observed to be a particularly stiff set of equations. Recently, it was demonstrated that the stiffness of the system could be relieved by rewriting the equations such that the potential is obtained from Ohm's law rather than Gauss's law while adding some source terms to the ion transport equation to ensure that Gauss's law is satisfied in non-neutral regions. Although the latter was applicable to multicomponent and multidimensional plasmas, it could not be used for plasmas in which the magnetic field was significant. This paper hence proposes a new computationally-efficient set of electron and ion transport equations that can be used not only for a plasma with multiple types of positive and negative ions, but also for a plasma in magnetic field. Because the proposed set of equations is obtained from the same physical model as the conventional drift-diffusion equations without introducing new assumptions or simplifications, it results in the same exact solution when the grid is refined sufficiently while being more computationally efficient: not only is the proposed approach considerably less stiff and hence requires fewer iterations to reach convergence but it yields a converged solution that exhibits a significantly higher resolution. The combined faster convergence and higher resolution is shown to result in a hundredfold increase in computational efficiency for some typical steady and unsteady plasma problems including non-neutral cathode and anode sheaths as well as quasi-neutral regions.
A new experimental approach to computer-aided face/skull identification in forensic anthropology.
Ricci, Alessio; Marella, Gian Luca; Apostol, Mario Alexandru
2006-03-01
The present study introduces a new approach to computer-assisted face/skull matching used for personal identification purposes in forensic anthropology. In this experiment, the authors formulated an algorithm able to identify the face of a person suspected to have disappeared, by comparing the respective person's facial image with the skull radiograph. A total of 14 subjects were selected for the study, from which a facial photograph and skull radiograph were taken and ultimately compiled into a database, saved to the hard drive of a computer. The photographs of the faces and corresponding skull radiographs were then drafted using common photographic software, taking caution not to alter the informational content of the images. Once computer generated, the facial images and menu were displayed on a color monitor. In the first phase, a few anatomic points of each photograph were selected and marked with a cross to facilitate and more accurately match the face with its corresponding skull. In the second phase, the above mentioned cross grid was superimposed on the radiographic image of the skull and brought to scale. In the third phase, the crosses were transferred to the cranial points of the radiograph. In the fourth phase, the algorithm calculated the distance of each transferred cross and the corresponding average. The smaller the mean value, the greater the index of similarity between the face and skull.A total of 196 cross-comparisons were conducted, with positive identification resulting in each case. Hence, the algorithm matched a facial photograph to the correct skull in 100% of the cases.
Methodical Approaches to Teaching of Computer Modeling in Computer Science Course
ERIC Educational Resources Information Center
Rakhimzhanova, B. Lyazzat; Issabayeva, N. Darazha; Khakimova, Tiyshtik; Bolyskhanova, J. Madina
2015-01-01
The purpose of this study was to justify of the formation technique of representation of modeling methodology at computer science lessons. The necessity of studying computer modeling is that the current trends of strengthening of general education and worldview functions of computer science define the necessity of additional research of the…
ERIC Educational Resources Information Center
Kay, Robin H.
1989-01-01
Describes study conducted at the University of Toronto that assessed the attitudes of student teachers toward computers by using a multicomponent model, the Computer Attitude Measure (CAM). Cognitive, affective, and behavioral attitudes are examined, and correlations of computer literacy, experience, and internal locus of control are discussed.…
Reflections on John Monaghan's "Computer Algebra, Instrumentation, and the Anthropological Approach"
ERIC Educational Resources Information Center
Blume, Glen
2007-01-01
Reactions to John Monaghan's "Computer Algebra, Instrumentation and the Anthropological Approach" focus on a variety of issues related to the ergonomic approach (instrumentation) and anthropological approach to mathematical activity and practice. These include uses of the term technique; several possibilities for integration of the two approaches;…
Reduced-Order Modeling: New Approaches for Computational Physics
NASA Technical Reports Server (NTRS)
Beran, Philip S.; Silva, Walter A.
2001-01-01
In this paper, we review the development of new reduced-order modeling techniques and discuss their applicability to various problems in computational physics. Emphasis is given to methods ba'sed on Volterra series representations and the proper orthogonal decomposition. Results are reported for different nonlinear systems to provide clear examples of the construction and use of reduced-order models, particularly in the multi-disciplinary field of computational aeroelasticity. Unsteady aerodynamic and aeroelastic behaviors of two- dimensional and three-dimensional geometries are described. Large increases in computational efficiency are obtained through the use of reduced-order models, thereby justifying the initial computational expense of constructing these models and inotivatim,- their use for multi-disciplinary design analysis.
Wolverton, Christopher; Ozolins, Vidvuds; Kung, Harold H.; Yang, Jun; Hwang, Sonjong; Shore, Sheldon
2016-11-28
The objective of the proposed program is to discover novel mixed hydrides for hydrogen storage, which enable the DOE 2010 system-level goals. Our goal is to find a material that desorbs 8.5 wt.% H_{2} or more at temperatures below 85°C. The research program will combine first-principles calculations of reaction thermodynamics and kinetics with material and catalyst synthesis, testing, and characterization. We will combine materials from distinct categories (e.g., chemical and complex hydrides) to form novel multicomponent reactions. Systems to be studied include mixtures of complex hydrides and chemical hydrides [e.g. LiNH^{2+}NH_{3}BH_{3}] and nitrogen-hydrogen based borohydrides [e.g. Al(BH_{4})_{3}(NH_{3})_{3}]. The 2010 and 2015 FreedomCAR/DOE targets for hydrogen storage systems are very challenging, and cannot be met with existing materials. The vast majority of the work to date has delineated materials into various classes, e.g., complex and metal hydrides, chemical hydrides, and sorbents. However, very recent studies indicate that mixtures of storage materials, particularly mixtures between various classes, hold promise to achieve technological attributes that materials within an individual class cannot reach. Our project involves a systematic, rational approach to designing novel multicomponent mixtures of materials with fast hydrogenation/dehydrogenation kinetics and favorable thermodynamics using a combination of state-of-the-art scientific computing and experimentation. We will use the accurate predictive power of first-principles modeling to understand the thermodynamic and microscopic kinetic processes involved in hydrogen release and uptake and to design new material/catalyst systems with improved properties. Detailed characterization and atomic-scale catalysis experiments will elucidate the effect of dopants and nanoscale catalysts in achieving fast kinetics and reversibility. And
AVES: A Computer Cluster System approach for INTEGRAL Scientific Analysis
NASA Astrophysics Data System (ADS)
Federici, M.; Martino, B. L.; Natalucci, L.; Umbertini, P.
The AVES computing system, based on an "Cluster" architecture is a fully integrated, low cost computing facility dedicated to the archiving and analysis of the INTEGRAL data. AVES is a modular system that uses the software resource manager (SLURM) and allows almost unlimited expandibility (65,536 nodes and hundreds of thousands of processors); actually is composed by 30 Personal Computers with Quad-Cores CPU able to reach the computing power of 300 Giga Flops (300x10{9} Floating point Operations Per Second), with 120 GB of RAM and 7.5 Tera Bytes (TB) of storage memory in UFS configuration plus 6 TB for users area. AVES was designed and built to solve growing problems raised from the analysis of the large data amount accumulated by the INTEGRAL mission (actually about 9 TB) and due to increase every year. The used analysis software is the OSA package, distributed by the ISDC in Geneva. This is a very complex package consisting of dozens of programs that can not be converted to parallel computing. To overcome this limitation we developed a series of programs to distribute the workload analysis on the various nodes making AVES automatically divide the analysis in N jobs sent to N cores. This solution thus produces a result similar to that obtained by the parallel computing configuration. In support of this we have developed tools that allow a flexible use of the scientific software and quality control of on-line data storing. The AVES software package is constituted by about 50 specific programs. Thus the whole computing time, compared to that provided by a Personal Computer with single processor, has been enhanced up to a factor 70.
An Object-Oriented Approach to Writing Computational Electromagnetics Codes
NASA Technical Reports Server (NTRS)
Zimmerman, Martin; Mallasch, Paul G.
1996-01-01
Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.
Computational challenges of structure-based approaches applied to HIV.
Forli, Stefano; Olson, Arthur J
2015-01-01
Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.
The Future of Computer-Based Toxicity Prediction:
Mechanism-Based Models vs. Information Mining Approaches
When we speak of computer-based toxicity prediction, we are generally referring to a broad array of approaches which rely primarily upon chemical structure ...
New Approaches to Quantum Computing using Nuclear Magnetic Resonance Spectroscopy
Colvin, M; Krishnan, V V
2003-02-07
The power of a quantum computer (QC) relies on the fundamental concept of the superposition in quantum mechanics and thus allowing an inherent large-scale parallelization of computation. In a QC, binary information embodied in a quantum system, such as spin degrees of freedom of a spin-1/2 particle forms the qubits (quantum mechanical bits), over which appropriate logical gates perform the computation. In classical computers, the basic unit of information is the bit, which can take a value of either 0 or 1. Bits are connected together by logic gates to form logic circuits to implement complex logical operations. The expansion of modern computers has been driven by the developments of faster, smaller and cheaper logic gates. As the size of the logic gates become smaller toward the level of atomic dimensions, the performance of such a system is no longer considered classical but is rather governed by quantum mechanics. Quantum computers offer the potentially superior prospect of solving computational problems that are intractable to classical computers such as efficient database searches and cryptography. A variety of algorithms have been developed recently, most notably Shor's algorithm for factorizing long numbers into prime factors in polynomial time and Grover's quantum search algorithm. The algorithms that were of only theoretical interest as recently, until several methods were proposed to build an experimental QC. These methods include, trapped ions, cavity-QED, coupled quantum dots, Josephson junctions, spin resonance transistors, linear optics and nuclear magnetic resonance. Nuclear magnetic resonance (NMR) is uniquely capable of constructing small QCs and several algorithms have been implemented successfully. NMR-QC differs from other implementations in one important way that it is not a single QC, but a statistical ensemble of them. Thus, quantum computing based on NMR is considered as ensemble quantum computing. In NMR quantum computing, the spins with
A Computational Approach to Qualitative Analysis in Large Textual Datasets
Evans, Michael S.
2014-01-01
In this paper I introduce computational techniques to extend qualitative analysis into the study of large textual datasets. I demonstrate these techniques by using probabilistic topic modeling to analyze a broad sample of 14,952 documents published in major American newspapers from 1980 through 2012. I show how computational data mining techniques can identify and evaluate the significance of qualitatively distinct subjects of discussion across a wide range of public discourse. I also show how examining large textual datasets with computational methods can overcome methodological limitations of conventional qualitative methods, such as how to measure the impact of particular cases on broader discourse, how to validate substantive inferences from small samples of textual data, and how to determine if identified cases are part of a consistent temporal pattern. PMID:24498398
Goecks, Jeremy; Nekrutenko, Anton; Taylor, James
2010-01-01
Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
Tichit, M; Barbottin, A; Makowski, D
2010-06-01
In response to environmental threats, numerous indicators have been developed to assess the impact of livestock farming systems on the environment. Some of them, notably those based on management practices have been reported to have low accuracy. This paper reports the results of a study aimed at assessing whether accuracy can be increased at a reasonable cost by mixing individual indicators into models. We focused on proxy indicators representing an alternative to the direct impact measurement on two grassland bird species, the lapwing Vanellus vanellus and the redshank Tringa totanus. Models were developed using stepwise selection procedures or Bayesian model averaging (BMA). Sensitivity, specificity, and probability of correctly ranking fields (area under the curve, AUC) were estimated for each individual indicator or model from observational data measured on 252 grazed plots during 2 years. The cost of implementation of each model was computed as a function of the number and types of input variables. Among all management indicators, 50% had an AUC lower than or equal to 0.50 and thus were not better than a random decision. Independently of the statistical procedure, models combining management indicators were always more accurate than individual indicators for lapwings only. In redshanks, models based either on BMA or some selection procedures were non-informative. Higher accuracy could be reached, for both species, with model mixing management and habitat indicators. However, this increase in accuracy was also associated with an increase in model cost. Models derived by BMA were more expensive and slightly less accurate than those derived with selection procedures. Analysing trade-offs between accuracy and cost of indicators opens promising application perspectives as time consuming and expensive indicators are likely to be of low practical utility.
Liu, Aiping; Li, Junning; Wang, Z. Jane; McKeown, Martin J.
2012-01-01
Graphical models appear well suited for inferring brain connectivity from fMRI data, as they can distinguish between direct and indirect brain connectivity. Nevertheless, biological interpretation requires not only that the multivariate time series are adequately modeled, but also that there is accurate error-control of the inferred edges. The PCfdr algorithm, which was developed by Li and Wang, was to provide a computationally efficient means to control the false discovery rate (FDR) of computed edges asymptotically. The original PCfdr algorithm was unable to accommodate a priori information about connectivity and was designed to infer connectivity from a single subject rather than a group of subjects. Here we extend the original PCfdr algorithm and propose a multisubject, error-rate-controlled brain connectivity modeling approach that allows incorporation of prior knowledge of connectivity. In simulations, we show that the two proposed extensions can still control the FDR around or below a specified threshold. When the proposed approach is applied to fMRI data in a Parkinson's disease study, we find robust group evidence of the disease-related changes, the compensatory changes, and the normalizing effect of L-dopa medication. The proposed method provides a robust, accurate, and practical method for the assessment of brain connectivity patterns from functional neuroimaging data. PMID:23251232
A Computer-based Approach to Analyzing a Patient Pool.
ERIC Educational Resources Information Center
Wooten, Ruth K.
1981-01-01
A computer system for analyzing a patient pool used by the division of dental hygiene at Virginia Commonwealth University is presented as a model for evaluating patient profiles. Descriptions of the various patient parameters are provided, and guidelines are presented to assist institutions considering such a system. (Author/MLW)
Statistical Learning of Phonetic Categories: Insights from a Computational Approach
ERIC Educational Resources Information Center
McMurray, Bob; Aslin, Richard N.; Toscano, Joseph C.
2009-01-01
Recent evidence (Maye, Werker & Gerken, 2002) suggests that statistical learning may be an important mechanism for the acquisition of phonetic categories in the infant's native language. We examined the sufficiency of this hypothesis and its implications for development by implementing a statistical learning mechanism in a computational model…
Computational Conceptual Change: An Explanation-Based Approach
2012-06-01
of human mental models, (2) our psychologically plausible model of analogical generalization can learn these models from examples, and (3) conceptual...four simulations. We simulate conceptual change in the domains of astronomy, biology, and force dynamics where examples of psychological conceptual...provide a consistent computational account of human mental models, (2) our psychologically plausible model of analogical generalization can learn these
One Instructor's Approach to Computer Assisted Instruction in General Chemistry.
ERIC Educational Resources Information Center
DeLorenzo, Ronald
1982-01-01
Discusses advantages of using computer-assisted instruction in a college general chemistry course. Advantages include using programs which generate random equations with double arrows (equilibrium systems) or generate alkane structural formula, asking for the correct IUPAC name of the structure. (Author/JN)
Modeling civil violence: An agent-based computational approach
Epstein, Joshua M.
2002-01-01
This article presents an agent-based computational model of civil violence. Two variants of the civil violence model are presented. In the first a central authority seeks to suppress decentralized rebellion. In the second a central authority seeks to suppress communal violence between two warring ethnic groups. PMID:11997450
Linguistics, Computers, and the Language Teacher. A Communicative Approach.
ERIC Educational Resources Information Center
Underwood, John H.
This analysis of the state of the art of computer programs and programming for language teaching has two parts. In the first part, an overview of the theory and practice of language teaching, Noam Chomsky's view of language, and the implications and problems of generative theory are presented. The theory behind the input model of language…
Computational Modelling and Simulation Fostering New Approaches in Learning Probability
ERIC Educational Resources Information Center
Kuhn, Markus; Hoppe, Ulrich; Lingnau, Andreas; Wichmann, Astrid
2006-01-01
Discovery learning in mathematics in the domain of probability based on hands-on experiments is normally limited because of the difficulty in providing sufficient materials and data volume in terms of repetitions of the experiments. Our cooperative, computational modelling and simulation environment engages students and teachers in composing and…
A "Service-Learning Approach" to Teaching Computer Graphics
ERIC Educational Resources Information Center
Hutzel, Karen
2007-01-01
The author taught a computer graphics course through a service-learning framework to undergraduate and graduate students in the spring of 2003 at Florida State University (FSU). The students in this course participated in learning a software program along with youths from a neighboring, low-income, primarily African-American community. Together,…
A New Approach: Computer-Assisted Problem-Solving Systems
ERIC Educational Resources Information Center
Gok, Tolga
2010-01-01
Computer-assisted problem solving systems are rapidly growing in educational use and with the advent of the Internet. These systems allow students to do their homework and solve problems online with the help of programs like Blackboard, WebAssign and LON-CAPA program etc. There are benefits and drawbacks of these systems. In this study, the…
ERIC Educational Resources Information Center
Zajenkowski, Marcin; Styla, Rafal; Szymanik, Jakub
2011-01-01
We compared the processing of natural language quantifiers in a group of patients with schizophrenia and a healthy control group. In both groups, the difficulty of the quantifiers was consistent with computational predictions, and patients with schizophrenia took more time to solve the problems. However, they were significantly less accurate only…
James, Conrad D.; Schiess, Adrian B.; Howell, Jamie; Baca, Michael J.; Partridge, L. Donald; Finnegan, Patrick Sean; Wolfley, Steven L.; Dagel, Daryl James; Spahn, Olga Blum; Harper, Jason C.; Pohl, Kenneth Roy; Mickel, Patrick R.; Lohn, Andrew; Marinella, Matthew
2013-10-01
The human brain (volume=1200cm3) consumes 20W and is capable of performing > 10^16 operations/s. Current supercomputer technology has reached 1015 operations/s, yet it requires 1500m^3 and 3MW, giving the brain a 10^12 advantage in operations/s/W/cm^3. Thus, to reach exascale computation, two achievements are required: 1) improved understanding of computation in biological tissue, and 2) a paradigm shift towards neuromorphic computing where hardware circuits mimic properties of neural tissue. To address 1), we will interrogate corticostriatal networks in mouse brain tissue slices, specifically with regard to their frequency filtering capabilities as a function of input stimulus. To address 2), we will instantiate biological computing characteristics such as multi-bit storage into hardware devices with future computational and memory applications. Resistive memory devices will be modeled, designed, and fabricated in the MESA facility in consultation with our internal and external collaborators.
Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.
Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao
2013-09-10
Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.
A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers
Carrillo, Jan-Michael Y.; Katsaras, John; Sumpter, Bobby G.; ...
2017-01-12
Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to signficant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally. Importantly, computer simulations are starting to play a more prominent role in interpreting experimental results, enabling a molecular under- standing of lipid membranes. Particularly, the synergymore » between scattering experiments and simulations offers opportunities for new discoveries in membrane physics, as the length and time scales probed by molecular dynamics (MD) simulations parallel those of experiments. We also describe a coarse-grained MD simulation approach that mimics neutron scattering data from large unilamellar lipid vesicles over a range of bilayer rigidity. Specfically, we simulate vesicle form factors and membrane thickness fluctuations determined from small angle neutron scattering (SANS) and neutron spin echo (NSE) experiments, respectively. Our simulations accurately reproduce trends from experiments and lay the groundwork for investigations of more complex membrane systems.« less
Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric
2016-01-01
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927
TOWARD HIGHLY SECURE AND AUTONOMIC COMPUTING SYSTEMS: A HIERARCHICAL APPROACH
Lee, Hsien-Hsin S
2010-05-11
The overall objective of this research project is to develop novel architectural techniques as well as system software to achieve a highly secure and intrusion-tolerant computing system. Such system will be autonomous, self-adapting, introspective, with self-healing capability under the circumstances of improper operations, abnormal workloads, and malicious attacks. The scope of this research includes: (1) System-wide, unified introspection techniques for autonomic systems, (2) Secure information-flow microarchitecture, (3) Memory-centric security architecture, (4) Authentication control and its implication to security, (5) Digital right management, (5) Microarchitectural denial-of-service attacks on shared resources. During the period of the project, we developed several architectural techniques and system software for achieving a robust, secure, and reliable computing system toward our goal.
Analytic reconstruction approach for parallel translational computed tomography.
Kong, Huihua; Yu, Hengyong
2015-01-01
To develop low-cost and low-dose computed tomography (CT) scanners for developing countries, recently a parallel translational computed tomography (PTCT) is proposed, and the source and detector are translated oppositely with respect to the imaging object without a slip-ring. In this paper, we develop an analytic filtered-backprojection (FBP)-type reconstruction algorithm for two dimensional (2D) fan-beam PTCT and extend it to three dimensional (3D) cone-beam geometry in a Feldkamp-type framework. Particularly, a weighting function is constructed to deal with data redundancy for multiple translations PTCT to eliminate image artifacts. Extensive numerical simulations are performed to validate and evaluate the proposed analytic reconstruction algorithms, and the results confirm their correctness and merits.
Computational approach to quantum encoder design for purity optimization
Yamamoto, Naoki; Fazel, Maryam
2007-07-15
In this paper, we address the problem of designing a quantum encoder that maximizes the minimum output purity of a given decohering channel, where the minimum is taken over all possible pure inputs. This problem is cast as a max-min optimization problem with a rank constraint on an appropriately defined matrix variable. The problem is computationally very hard because it is nonconvex with respect to both the objective function (output purity) and the rank constraint. Despite this difficulty, we provide a tractable computational algorithm that produces the exact optimal solution for codespace of dimension 2. Moreover, this algorithm is easily extended to cover the general class of codespaces, in which case the solution is suboptimal in the sense that the suboptimized output purity serves as a lower bound of the exact optimal purity. The algorithm consists of a sequence of semidefinite programmings and can be performed easily. Two typical quantum error channels are investigated to illustrate the effectiveness of our method.
Optimization of a DPI Inhaler: A Computational Approach.
Milenkovic, Jovana; Alexopoulos, Aleck H; Kiparissides, Costas
2017-03-01
Alternate geometries of a commercial dry powder inhaler (DPI, i.e., Turbuhaler; AstraZeneca, London, UK) are proposed based on the simulation results obtained from a fluid and particle dynamic computational model, previously developed by Milenkovic et al. The alternate DPI geometries are constructed by simple alterations to components of the commercial inhaler device leading to smoother flow patterns in regions where significant particle-wall collisions occur. The modified DPIs are investigated under the same conditions of the original studies of Milenkovic et al. for a wide range of inhalation flow rates (i.e., 30-70 L/min). Based on the computational results in terms of total particle deposition and fine particle fraction, the modified DPIs were improved over the original design of the commercial device.
Probing Cosmic Infrared Sources: A Computer Modeling Approach
1992-06-01
Bits and Bytes.", NASA Goddard Space Right Center, Green Belt , Maryland (May 1990). 11. "Probing Infrared Sources by Computer Modeling.", review talk...is this expected from elementary theory, but many observations can be well described with this assumption ( Kuiper 1967; Kwok 1980; Sopka et al. 1985...Neugebauer, H. J. Habing, P. E. Clegg, & T. J. Chester (Washington: GPO) Kuiper , T. B. H. et al. 1976, Api, 204, 408 Kwan, J., Scoville, N. 1976, Api, 209, 102
A User Modelling Approach for Computer-Based Critiquing
1990-01-01
9.1.2 Explicit Acquisition Methods ................. 176 9.1.3 Tutoring-based Methods ..................... 177 9.1.4 Statistical Analysis of User’s...accomplish the second process are the subject of this research . Cooperative problem solving systems assume that the third process is inherent in the...process of human-computer interaction. The second class of models above are psychological models developed by and for the analysis of human behavior
Modeling Cu2+-Aβ complexes from computational approaches
NASA Astrophysics Data System (ADS)
Alí-Torres, Jorge; Mirats, Andrea; Maréchal, Jean-Didier; Rodríguez-Santiago, Luis; Sodupe, Mariona
2015-09-01
Amyloid plaques formation and oxidative stress are two key events in the pathology of the Alzheimer disease (AD), in which metal cations have been shown to play an important role. In particular, the interaction of the redox active Cu2+ metal cation with Aβ has been found to interfere in amyloid aggregation and to lead to reactive oxygen species (ROS). A detailed knowledge of the electronic and molecular structure of Cu2+-Aβ complexes is thus important to get a better understanding of the role of these complexes in the development and progression of the AD disease. The computational treatment of these systems requires a combination of several available computational methodologies, because two fundamental aspects have to be addressed: the metal coordination sphere and the conformation adopted by the peptide upon copper binding. In this paper we review the main computational strategies used to deal with the Cu2+-Aβ coordination and build plausible Cu2+-Aβ models that will afterwards allow determining physicochemical properties of interest, such as their redox potential.
Computational Approaches to Viral Evolution and Rational Vaccine Design
NASA Astrophysics Data System (ADS)
Bhattacharya, Tanmoy
2006-10-01
Viral pandemics, including HIV, are a major health concern across the world. Experimental techniques available today have uncovered a great wealth of information about how these viruses infect, grow, and cause disease; as well as how our body attempts to defend itself against them. Nevertheless, due to the high variability and fast evolution of many of these viruses, the traditional method of developing vaccines by presenting a heuristically chosen strain to the body fails and an effective intervention strategy still eludes us. A large amount of carefully curated genomic data on a number of these viruses are now available, often annotated with disease and immunological context. The availability of parallel computers has now made it possible to carry out a systematic analysis of this data within an evolutionary framework. I will describe, as an example, how computations on such data has allowed us to understand the origins and diversification of HIV, the causative agent of AIDS. On the practical side, computations on the same data is now being used to inform choice or defign of optimal vaccine strains.
Computational Approaches to RNA Structure Prediction, Analysis and Design
Laing, Christian; Schlick, Tamar
2011-01-01
RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires RNA tertiary structure knowledge. While modeling approaches for the study of RNA structures and dynamics lag behind efforts in protein folding, much progress has been achieved in the past two years. Here, we review recent advances in RNA folding algorithms, RNA tertiary motif discovery, applications of graph theory approaches to RNA structure and function, and in silico generation of RNA sequence pools for aptamer design. Advances within each area can be combined to impact many problems in RNA structure and function. PMID:21514143
Computational approach for calculating bound states in quantum field theory
NASA Astrophysics Data System (ADS)
Lv, Q. Z.; Norris, S.; Brennan, R.; Stefanovich, E.; Su, Q.; Grobe, R.
2016-09-01
We propose a nonperturbative approach to calculate bound-state energies and wave functions for quantum field theoretical models. It is based on the direct diagonalization of the corresponding quantum field theoretical Hamiltonian in an effectively discretized and truncated Hilbert space. We illustrate this approach for a Yukawa-like interaction between fermions and bosons in one spatial dimension and show where it agrees with the traditional method based on the potential picture and where it deviates due to recoil and radiative corrections. This method permits us also to obtain some insight into the spatial characteristics of the distribution of the fermions in the ground state, such as the bremsstrahlung-induced widening.
Workflow Scheduling in Grid Computing Environment using a Hybrid GAACO Approach
NASA Astrophysics Data System (ADS)
Sathish, Kuppani; RamaMohan Reddy, A.
2016-06-01
In recent trends, grid computing is one of the emerging areas in computing platform which supports parallel and distributed environments. The main problem for grid computing is scheduling of workflows in terms of user specifications is a stimulating task and it also impacts the performance. This paper proposes a hybrid GAACO approach, which is a combination of Genetic Algorithm and Ant Colony Optimization Algorithm. The GAACO approach proposes different types of scheduling heuristics for the grid environment. The main objective of this approach is to satisfy all the defined constraints and user parameters.
Workflow Scheduling in Grid Computing Environment using a Hybrid GAACO Approach
NASA Astrophysics Data System (ADS)
Sathish, Kuppani; RamaMohan Reddy, A.
2017-02-01
In recent trends, grid computing is one of the emerging areas in computing platform which supports parallel and distributed environments. The main problem for grid computing is scheduling of workflows in terms of user specifications is a stimulating task and it also impacts the performance. This paper proposes a hybrid GAACO approach, which is a combination of Genetic Algorithm and Ant Colony Optimization Algorithm. The GAACO approach proposes different types of scheduling heuristics for the grid environment. The main objective of this approach is to satisfy all the defined constraints and user parameters.
Computer-aided diagnostic approach of dermoscopy images acquiring relevant features
NASA Astrophysics Data System (ADS)
Castillejos-Fernández, H.; Franco-Arcega, A.; López-Ortega, O.
2016-09-01
In skin cancer detection, automated analysis of borders, colors, and structures of a lesion relies upon an accurate segmentation process and it is an important first step in any Computer-Aided Diagnosis (CAD) system. However, irregular and disperse lesion borders, low contrast, artifacts in images and variety of colors within the interest region make the problem difficult. In this paper, we propose an efficient approach of automatic classification which considers specific lesion features. First, for the selection of lesion skin we employ the segmentation algorithm W-FCM.1 Then, in the feature extraction stage we consider several aspects: the area of the lesion, which is calculated by correlating axes and we calculate the specific the value of asymmetry in both axes. For color analysis we employ an ensemble of clusterers including K-Means, Fuzzy K-Means and Kohonep maps, all of which estimate the presence of one or more colors defined in ABCD rule and the values for each of the segmented colors. Another aspect to consider is the type of structures that appear in the lesion Those are defined by using the ell-known GLCM method. During the classification stage we compare several methods in order to define if the lesion is benign or malignant. An important contribution of the current approach in segmentation-classification problem resides in the use of information from all color channels together, as well as the measure of each color in the lesion and the axes correlation. The segmentation and classification measures have been performed using sensibility, specificity, accuracy and AUC metric over a set of dermoscopy images from ISDIS data set
Accurate ab Initio Spin Densities.
Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus
2012-06-12
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].
A computer simulation approach to measurement of human control strategy
NASA Technical Reports Server (NTRS)
Green, J.; Davenport, E. L.; Engler, H. F.; Sears, W. E., III
1982-01-01
Human control strategy is measured through use of a psychologically-based computer simulation which reflects a broader theory of control behavior. The simulation is called the human operator performance emulator, or HOPE. HOPE was designed to emulate control learning in a one-dimensional preview tracking task and to measure control strategy in that setting. When given a numerical representation of a track and information about current position in relation to that track, HOPE generates positions for a stick controlling the cursor to be moved along the track. In other words, HOPE generates control stick behavior corresponding to that which might be used by a person learning preview tracking.
A complex systems approach to computational molecular biology
Lapedes, A. |
1993-09-01
We report on the containing research program at Santa Fe Institute that applies complex systems methodology to computational molecular biology. Two aspects are stressed here are the use of co-evolving adaptive neutral networks for determining predictable protein structure classifications, and the use of information theory to elucidate protein structure and function. A ``snapshot`` of the current state of research in these two topics is presented, representing the present state of two major research thrusts in the program of Genetic Data and Sequence Analysis at the Santa Fe Institute.
NEW APPROACHES: Physics with a car headlamp and a computer
NASA Astrophysics Data System (ADS)
Cooper, Ian
1997-05-01
An experiment suitable for high school students or undergraduates uses a car headlamp. With the use of a spreadsheet program, extensive data manipulation becomes a simple task, enabling students to answer relevant questions as opposed to just verifying a well-known law. By using the computer in this way, students can be given an awareness of many mathematical techniques used in data analysis not otherwise possible because of time constraints or students' lack of knowledge. Templates of varying degrees of complexity can be used to cater for different groups of students.
Computational Approaches to Enhance Nanosafety and Advance Nanomedicine
NASA Astrophysics Data System (ADS)
Mendoza, Eduardo R.
With the increasing use of nanoparticles in food processing, filtration/purification and consumer products, as well as the huge potential of their use in nanomedicine, a quantitative understanding of the effects of nanoparticle uptake and transport is needed. We provide examples of novel methods for modeling complex bio-nano interactions which are based on stochastic process algebras. Since model construction presumes sufficient availability of experimental data, recent developments in "nanoinformatics", an emerging discipline analogous to bioinfomatics, in building an accessible information infrastructure are subsequently discussed. Both computational areas offer opportunities for Filipinos to engage in collaborative, cutting edge research in this impactful field.
Cognitive control in majority search: a computational modeling approach.
Wang, Hongbin; Liu, Xun; Fan, Jin
2011-01-01
Despite the importance of cognitive control in many cognitive tasks involving uncertainty, the computational mechanisms of cognitive control in response to uncertainty remain unclear. In this study, we develop biologically realistic neural network models to investigate the instantiation of cognitive control in a majority function task, where one determines the category to which the majority of items in a group belong. Two models are constructed, both of which include the same set of modules representing task-relevant brain functions and share the same model structure. However, with a critical change of a model parameter setting, the two models implement two different underlying algorithms: one for grouping search (where a subgroup of items are sampled and re-sampled until a congruent sample is found) and the other for self-terminating search (where the items are scanned and counted one-by-one until the majority is decided). The two algorithms hold distinct implications for the involvement of cognitive control. The modeling results show that while both models are able to perform the task, the grouping search model fit the human data better than the self-terminating search model. An examination of the dynamics underlying model performance reveals how cognitive control might be instantiated in the brain for computing the majority function.
A uniform approach for programming distributed heterogeneous computing systems
Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas
2014-01-01
Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015
A uniform approach for programming distributed heterogeneous computing systems.
Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas
2014-12-01
Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater's performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations.
Computational approaches for inferring the functions of intrinsically disordered proteins
Varadi, Mihaly; Vranken, Wim; Guharoy, Mainak; Tompa, Peter
2015-01-01
Intrinsically disordered proteins (IDPs) are ubiquitously involved in cellular processes and often implicated in human pathological conditions. The critical biological roles of these proteins, despite not adopting a well-defined fold, encouraged structural biologists to revisit their views on the protein structure-function paradigm. Unfortunately, investigating the characteristics and describing the structural behavior of IDPs is far from trivial, and inferring the function(s) of a disordered protein region remains a major challenge. Computational methods have proven particularly relevant for studying IDPs: on the sequence level their dependence on distinct characteristics determined by the local amino acid context makes sequence-based prediction algorithms viable and reliable tools for large scale analyses, while on the structure level the in silico integration of fundamentally different experimental data types is essential to describe the behavior of a flexible protein chain. Here, we offer an overview of the latest developments and computational techniques that aim to uncover how protein function is connected to intrinsic disorder. PMID:26301226
Cognitive Control in Majority Search: A Computational Modeling Approach
Wang, Hongbin; Liu, Xun; Fan, Jin
2011-01-01
Despite the importance of cognitive control in many cognitive tasks involving uncertainty, the computational mechanisms of cognitive control in response to uncertainty remain unclear. In this study, we develop biologically realistic neural network models to investigate the instantiation of cognitive control in a majority function task, where one determines the category to which the majority of items in a group belong. Two models are constructed, both of which include the same set of modules representing task-relevant brain functions and share the same model structure. However, with a critical change of a model parameter setting, the two models implement two different underlying algorithms: one for grouping search (where a subgroup of items are sampled and re-sampled until a congruent sample is found) and the other for self-terminating search (where the items are scanned and counted one-by-one until the majority is decided). The two algorithms hold distinct implications for the involvement of cognitive control. The modeling results show that while both models are able to perform the task, the grouping search model fit the human data better than the self-terminating search model. An examination of the dynamics underlying model performance reveals how cognitive control might be instantiated in the brain for computing the majority function. PMID:21369357
Nicholson, Anita; Tobin, Mary
2006-01-01
This presentation will discuss coupling commercial and customized computer-supported teaching aids to provide BSN nursing students with a friendly customer-centered self-study approach to psychomotor skill acquisition.
Environmental models are products of the computer architecture and software tools available at the time of development. Scientifically sound algorithms may persist in their original state even as system architectures and software development approaches evolve and progress. Dating...
NASA Astrophysics Data System (ADS)
Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando
2015-07-01
We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.
Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando
2015-07-21
We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach
Eslami-Mossallam, Behrouz; Schram, Raoul D.; Tompitak, Marco; van Noort, John; Schiessel, Helmut
2016-01-01
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function. PMID:27272176
Computational biology approach to uncover hepatitis C virus helicase operation
Flechsig, Holger
2014-01-01
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings. PMID:24707123
A computational approach to the twin paradox in curved spacetime
NASA Astrophysics Data System (ADS)
Fung, Kenneth K. H.; Clark, Hamish A.; Lewis, Geraint F.; Wu, Xiaofeng
2016-09-01
Despite being a major component in the teaching of special relativity, the twin ‘paradox’ is generally not examined in courses on general relativity. Due to the complexity of analytical solutions to the problem, the paradox is often neglected entirely, and students are left with an incomplete understanding of the relativistic behaviour of time. This article outlines a project, undertaken by undergraduate physics students at the University of Sydney, in which a novel computational method was derived in order to predict the time experienced by a twin following a number of paths between two given spacetime coordinates. By utilising this method, it is possible to make clear to students that following a geodesic in curved spacetime does not always result in the greatest experienced proper time.
Economic growth rate management by soft computing approach
NASA Astrophysics Data System (ADS)
Maksimović, Goran; Jović, Srđan; Jovanović, Radomir
2017-01-01
Economic growth rate management is very important process in order to improve the economic stability of any country. The main goal of the study was to manage the impact of agriculture, manufacturing, industry and services on the economic growth rate prediction. Soft computing methodology was used in order to select the inputs influence on the economic growth rate prediction. It is known that the economic growth may be developed on the basis of combination of different factors. Gross domestic product (GDP) was used as economic growth indicator. It was found services have the highest impact on the GDP growth rate. On the contrary, the manufacturing has the smallest impact on the GDP growth rate.
Computational biology approach to uncover hepatitis C virus helicase operation.
Flechsig, Holger
2014-04-07
Hepatitis C virus (HCV) helicase is a molecular motor that splits nucleic acid duplex structures during viral replication, therefore representing a promising target for antiviral treatment. Hence, a detailed understanding of the mechanism by which it operates would facilitate the development of efficient drug-assisted therapies aiming to inhibit helicase activity. Despite extensive investigations performed in the past, a thorough understanding of the activity of this important protein was lacking since the underlying internal conformational motions could not be resolved. Here we review investigations that have been previously performed by us for HCV helicase. Using methods of structure-based computational modelling it became possible to follow entire operation cycles of this motor protein in structurally resolved simulations and uncover the mechanism by which it moves along the nucleic acid and accomplishes strand separation. We also discuss observations from that study in the light of recent experimental studies that confirm our findings.
Fu, Huili; Ji, Zhongyin; Chen, Xuejie; Cheng, Anwei; Liu, Shucheng; Gong, Peiwei; Li, Guoliang; Chen, Guang; Sun, Zhiwei; Zhao, Xianen; Cheng, Feng; You, Jinmao
2017-03-01
Herein, we first reported a facile synthesis method for fabrication of highly photoluminescent carbon quantum dots (CQDs) using sodium alginate as the carbon source and histidine as both the nitrogen source and functional monomer by one-pot hydrothermal synthesis. The as-prepared CQDs gave a high quantum yield of 32%. By employing the new CQDs and rhodamine B (RhB), we demonstrated a simple, facile, sensitive, and accurate ratiometric sensor for detection of Hg(2+) and biological thiols. The photoluminescence of CQDs in the ratiometric sensor can be selectively and intensively suppressed by Hg(2+) due to strong electrostatic interaction between the surface functional groups of the CQDs and Hg(2+). When glutathione (GSH) was introduced into the "Turn Off" CQDs-RhB-Hg(2+) sensing system, the fluorescence of the CQDs can be recovered rapidly due to the stronger affinity between thiol and Hg(2+), while the fluorescence of the RhB remained constant in this sensing process. Based on the above principle, the ratiometric strategy for detecting Hg(2+) and GSH can be achieved readily, and gives satisfactory limit of detections (LODs) of 30 and 20 nM for Hg(2+) and GSH, respectively. The dual-emission fluorescent CQDs-RhB sensor does not need the complicated molecular design and the synthesis of dual-emission fluorophores. Meanwhile, the feasibility of the proposed method for analysis of water samples, food samples, and biological samples (plasma from mice oxidative stress study) was investigated. The developed ratiometric nanosensor is proven to be facile, with less sample consumption, rapid, lost cost, highly sensitive, and very selective for Hg(2+) and biological thiol detection, which offers a new approach for environmental, food, and biological analysis. Graphical abstract Ratiometric nanosensing approach detection of Hg(2+) and biological thiols.
Perturbation approach for nuclear magnetic resonance solid-state quantum computation
Berman, G. P.; Kamenev, D. I.; Tsifrinovich, V. I.
2003-01-01
A dynmore » amics of a nuclear-spin quantum computer with a large number ( L = 1000 ) of qubits is considered using a perturbation approach. Small parameters are introduced and used to compute the error in an implementation of an entanglement between remote qubits, using a sequence of radio-frequency pulses. The error is computed up to the different orders of the perturbation theory and tested using exact numerical solution.« less
Computational s-block thermochemistry with the correlation consistent composite approach.
DeYonker, Nathan J; Ho, Dustin S; Wilson, Angela K; Cundari, Thomas R
2007-10-25
The correlation consistent composite approach (ccCA) is a model chemistry that has been shown to accurately compute gas-phase enthalpies of formation for alkali and alkaline earth metal oxides and hydroxides (Ho, D. S.; DeYonker, N. J.; Wilson, A. K.; Cundari, T. R. J. Phys. Chem. A 2006, 110, 9767). The ccCA results contrast to more widely used model chemistries where calculated enthalpies of formation for such species can be in error by up to 90 kcal mol-1. In this study, we have applied ccCA to a more general set of 42 s-block molecules and compared the ccCA DeltaHf values to values obtained using the G3 and G3B model chemistries. Included in this training set are water complexes such as Na(H2O)n+ where n = 1 - 4, dimers and trimers of ionic compounds such as (LiCl)2 and (LiCl)3, and the largest ccCA computation to date: Be(acac)2, BeC10H14O4. Problems with the G3 model chemistries seem to be isolated to metal-oxygen bonded systems and Be-containing systems, as G3 and G3B still perform quite well with a 2.7 and 2.6 kcal mol-1 mean absolute deviation (MAD), respectively, for gas-phase enthalpies of formation. The MAD of the ccCA is only 2.2 kcal mol-1 for enthalpies of formation (DeltaHf) for all compounds studied herein. While this MAD is roughly double that found for a ccCA study of >350 main group (i.e., p-block) compounds, it is commensurate with typical experimental uncertainties for s-block complexes. Some molecules where G3/G3B and ccCA computed DeltaHf values deviate significantly from experiment, such as (LiCl)3, NaCN, and MgF, are inviting candidates for new experimental and high-level theoretical studies.
Cai, C.; Rodet, T.; Mohammad-Djafari, A.; Legoupil, S.
2013-11-15
Purpose: Dual-energy computed tomography (DECT) makes it possible to get two fractions of basis materials without segmentation. One is the soft-tissue equivalent water fraction and the other is the hard-matter equivalent bone fraction. Practical DECT measurements are usually obtained with polychromatic x-ray beams. Existing reconstruction approaches based on linear forward models without counting the beam polychromaticity fail to estimate the correct decomposition fractions and result in beam-hardening artifacts (BHA). The existing BHA correction approaches either need to refer to calibration measurements or suffer from the noise amplification caused by the negative-log preprocessing and the ill-conditioned water and bone separation problem. To overcome these problems, statistical DECT reconstruction approaches based on nonlinear forward models counting the beam polychromaticity show great potential for giving accurate fraction images.Methods: This work proposes a full-spectral Bayesian reconstruction approach which allows the reconstruction of high quality fraction images from ordinary polychromatic measurements. This approach is based on a Gaussian noise model with unknown variance assigned directly to the projections without taking negative-log. Referring to Bayesian inferences, the decomposition fractions and observation variance are estimated by using the joint maximum a posteriori (MAP) estimation method. Subject to an adaptive prior model assigned to the variance, the joint estimation problem is then simplified into a single estimation problem. It transforms the joint MAP estimation problem into a minimization problem with a nonquadratic cost function. To solve it, the use of a monotone conjugate gradient algorithm with suboptimal descent steps is proposed.Results: The performance of the proposed approach is analyzed with both simulated and experimental data. The results show that the proposed Bayesian approach is robust to noise and materials. It is also
Pierri, Ciro Leonardo; Parisi, Giovanni; Porcelli, Vito
2010-09-01
The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.
Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach
Herd, Seth A.; Krueger, Kai A.; Kriete, Trenton E.; Huang, Tsung-Ren; Hazy, Thomas E.; O'Reilly, Randall C.
2013-01-01
We address strategic cognitive sequencing, the “outer loop” of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC) and basal ganglia (BG) cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or “self-instruction”). The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a “bridging” state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area. PMID:23935605
Non-racemic mixture model: a computational approach.
Polanco, Carlos; Buhse, Thomas
2017-01-01
The behavior of a slight chiral bias in favor of l-amino acids over d-amino acids was studied in an evolutionary mathematical model generating mixed chiral peptide hexamers. The simulations aimed to reproduce a very generalized prebiotic scenario involving a specified couple of amino acid enantiomers and a possible asymmetric amplification through autocatalytic peptide self-replication while forming small multimers of a defined length. Our simplified model allowed the observation of a small ascending but not conclusive tendency in the l-amino acid over the d-amino acid profile for the resulting mixed chiral hexamers in computer simulations of 100 peptide generations. This simulation was carried out by changing the chiral bias from 1% to 3%, in three stages of 15, 50 and 100 generations to observe any alteration that could mean a drastic change in behavior. So far, our simulations lead to the assumption that under the exposure of very slight non-racemic conditions, a significant bias between l- and d-amino acids, as present in our biosphere, was unlikely generated under prebiotic conditions if autocatalytic peptide self-replication was the main or the only driving force of chiral auto-amplification.
Localized tissue mineralization regulated by bone remodelling: A computational approach
Decco, Oscar; Adams, George; Cook, Richard B.; García Aznar, José Manuel
2017-01-01
Bone is a living tissue whose main mechanical function is to provide stiffness, strength and protection to the body. Both stiffness and strength depend on the mineralization of the organic matrix, which is constantly being remodelled by the coordinated action of the bone multicellular units (BMUs). Due to the dynamics of both remodelling and mineralization, each sample of bone is composed of structural units (osteons in cortical and packets in cancellous bone) created at different times, therefore presenting different levels of mineral content. In this work, a computational model is used to understand the feedback between the remodelling and the mineralization processes under different load conditions and bone porosities. This model considers that osteoclasts primarily resorb those parts of bone closer to the surface, which are younger and less mineralized than older inner ones. Under equilibrium loads, results show that bone volumes with both the highest and the lowest levels of porosity (cancellous and cortical respectively) tend to develop higher levels of mineral content compared to volumes with intermediate porosity, thus presenting higher material densities. In good agreement with recent experimental measurements, a boomerang-like pattern emerges when plotting apparent density at the tissue level versus material density at the bone material level. Overload and disuse states are studied too, resulting in a translation of the apparent–material density curve. Numerical results are discussed pointing to potential clinical applications. PMID:28306746
Localized tissue mineralization regulated by bone remodelling: A computational approach.
Berli, Marcelo; Borau, Carlos; Decco, Oscar; Adams, George; Cook, Richard B; García Aznar, José Manuel; Zioupos, Peter
2017-01-01
Bone is a living tissue whose main mechanical function is to provide stiffness, strength and protection to the body. Both stiffness and strength depend on the mineralization of the organic matrix, which is constantly being remodelled by the coordinated action of the bone multicellular units (BMUs). Due to the dynamics of both remodelling and mineralization, each sample of bone is composed of structural units (osteons in cortical and packets in cancellous bone) created at different times, therefore presenting different levels of mineral content. In this work, a computational model is used to understand the feedback between the remodelling and the mineralization processes under different load conditions and bone porosities. This model considers that osteoclasts primarily resorb those parts of bone closer to the surface, which are younger and less mineralized than older inner ones. Under equilibrium loads, results show that bone volumes with both the highest and the lowest levels of porosity (cancellous and cortical respectively) tend to develop higher levels of mineral content compared to volumes with intermediate porosity, thus presenting higher material densities. In good agreement with recent experimental measurements, a boomerang-like pattern emerges when plotting apparent density at the tissue level versus material density at the bone material level. Overload and disuse states are studied too, resulting in a translation of the apparent-material density curve. Numerical results are discussed pointing to potential clinical applications.
TOPICAL REVIEW: Computational approaches to 3D modeling of RNA
NASA Astrophysics Data System (ADS)
Laing, Christian; Schlick, Tamar
2010-07-01
Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research.
Computer Mediated Social Network Approach to Software Support and Maintenance
2010-06-01
mathematics (Euler, 1741; Sachs, Stiebitz, & Wilson, 1988), philosophy ( Durkheim , 2001), the social science domain (Granovetter 1973; 1983; Milgram, 1967...to philosophy ( Durkheim , 2001), to the strength of the connections a (Granovetter 1973; Granovetter, 1983) and the number of connections (Milgram...Qualitative, quantitative, and mixed method approaches (Second ed.) Sage Publications Inc. Durkheim , É. (2001). The elementary forms of religious life, New
A Computational Approach to Estimating Nondisjunction Frequency in Saccharomyces cerevisiae
Chu, Daniel B.; Burgess, Sean M.
2016-01-01
Errors segregating homologous chromosomes during meiosis result in aneuploid gametes and are the largest contributing factor to birth defects and spontaneous abortions in humans. Saccharomyces cerevisiae has long served as a model organism for studying the gene network supporting normal chromosome segregation. Measuring homolog nondisjunction frequencies is laborious, and involves dissecting thousands of tetrads to detect missegregation of individually marked chromosomes. Here we describe a computational method (TetFit) to estimate the relative contributions of meiosis I nondisjunction and random-spore death to spore inviability in wild type and mutant strains. These values are based on finding the best-fit distribution of 4, 3, 2, 1, and 0 viable-spore tetrads to an observed distribution. Using TetFit, we found that meiosis I nondisjunction is an intrinsic component of spore inviability in wild-type strains. We show proof-of-principle that the calculated average meiosis I nondisjunction frequency determined by TetFit closely matches empirically determined values in mutant strains. Using these published data sets, TetFit uncovered two classes of mutants: Class A mutants skew toward increased nondisjunction death, and include those with known defects in establishing pairing, recombination, and/or synapsis of homologous chromosomes. Class B mutants skew toward random spore death, and include those with defects in sister-chromatid cohesion and centromere function. Epistasis analysis using TetFit is facilitated by the low numbers of tetrads (as few as 200) required to compare the contributions to spore death in different mutant backgrounds. TetFit analysis does not require any special strain construction, and can be applied to previously observed tetrad distributions. PMID:26747203
NASA Astrophysics Data System (ADS)
Wang, Mengyu; Brigham, John C.
2017-03-01
A computationally efficient gradient-based optimization approach for inverse material characterization from incomplete system response measurements that can utilize a generally applicable parameterization (e.g., finite element-type parameterization) is presented and evaluated. The key to this inverse characterization algorithm is the use of a direct inversion strategy with Gappy proper orthogonal decomposition (POD) response field estimation to initialize the inverse solution estimate prior to gradient-based optimization. Gappy POD is used to estimate the complete (i.e., all components over the entire spatial domain) system response field from incomplete (e.g., partial spatial distribution) measurements obtained from some type of system testing along with some amount of a priori information regarding the potential distribution of the unknown material property. The estimated complete system response is used within a physics-based direct inversion procedure with a finite element-type parameterization to estimate the spatial distribution of the desired unknown material property with minimal computational expense. Then, this estimated spatial distribution of the unknown material property is used to initialize a gradient-based optimization approach, which uses the adjoint method for computationally efficient gradient calculations, to produce the final estimate of the material property distribution. The three-step [(1) Gappy POD, (2) direct inversion, and (3) gradient-based optimization] inverse characterization approach is evaluated through simulated test problems based on the characterization of elastic modulus distributions with localized variations (e.g., inclusions) within simple structures. Overall, this inverse characterization approach is shown to efficiently and consistently provide accurate inverse characterization estimates for material property distributions from incomplete response field measurements. Moreover, the solution procedure is shown to be capable
An integrative computational approach for prioritization of genomic variants
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; Meydan, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; Paciorkowski, Alex R.; Mirzaa, Ghayda M.; Dave, Paul; Agam, Gady; Xu, Jinbo; Al-Gazali, Lihadh; Mason, Christopher E.; Ross, M. Elizabeth; Maltsev, Natalia; Gilliam, T. Conrad; Huang, Qingyang
2014-12-15
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.
An integrative computational approach for prioritization of genomic variants
Dubchak, Inna; Balasubramanian, Sandhya; Wang, Sheng; ...
2014-12-15
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidatemore » genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest.« less
Driving profile modeling and recognition based on soft computing approach.
Wahab, Abdul; Quek, Chai; Tan, Chin Keong; Takeda, Kazuya
2009-04-01
Advancements in biometrics-based authentication have led to its increasing prominence and are being incorporated into everyday tasks. Existing vehicle security systems rely only on alarms or smart card as forms of protection. A biometric driver recognition system utilizing driving behaviors is a highly novel and personalized approach and could be incorporated into existing vehicle security system to form a multimodal identification system and offer a greater degree of multilevel protection. In this paper, detailed studies have been conducted to model individual driving behavior in order to identify features that may be efficiently and effectively used to profile each driver. Feature extraction techniques based on Gaussian mixture models (GMMs) are proposed and implemented. Features extracted from the accelerator and brake pedal pressure were then used as inputs to a fuzzy neural network (FNN) system to ascertain the identity of the driver. Two fuzzy neural networks, namely, the evolving fuzzy neural network (EFuNN) and the adaptive network-based fuzzy inference system (ANFIS), are used to demonstrate the viability of the two proposed feature extraction techniques. The performances were compared against an artificial neural network (NN) implementation using the multilayer perceptron (MLP) network and a statistical method based on the GMM. Extensive testing was conducted and the results show great potential in the use of the FNN for real-time driver identification and verification. In addition, the profiling of driver behaviors has numerous other potential applications for use by law enforcement and companies dealing with buses and truck drivers.
An Integrative Computational Approach for Prioritization of Genomic Variants
Wang, Sheng; Meyden, Cem; Sulakhe, Dinanath; Poliakov, Alexander; Börnigen, Daniela; Xie, Bingqing; Taylor, Andrew; Ma, Jianzhu; Paciorkowski, Alex R.; Mirzaa, Ghayda M.; Dave, Paul; Agam, Gady; Xu, Jinbo; Al-Gazali, Lihadh; Mason, Christopher E.; Ross, M. Elizabeth; Maltsev, Natalia; Gilliam, T. Conrad
2014-01-01
An essential step in the discovery of molecular mechanisms contributing to disease phenotypes and efficient experimental planning is the development of weighted hypotheses that estimate the functional effects of sequence variants discovered by high-throughput genomics. With the increasing specialization of the bioinformatics resources, creating analytical workflows that seamlessly integrate data and bioinformatics tools developed by multiple groups becomes inevitable. Here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the Lynx platform, VISTA RViewer, the Developmental Brain Disorders Database (DBDB), and the RaptorX server, for the identification of high-confidence candidate genes contributing to pathogenesis of spina bifida. The analysis resulted in prediction and validation of deleterious mutations in the SLC19A placental transporter in mothers of the affected children that causes narrowing of the outlet channel and therefore leads to the reduced folate permeation rate. The described approach also enabled correct identification of several genes, previously shown to contribute to pathogenesis of spina bifida, and suggestion of additional genes for experimental validations. The study demonstrates that the seamless integration of bioinformatics resources enables fast and efficient prioritization and characterization of genomic factors and molecular networks contributing to the phenotypes of interest. PMID:25506935
Effects of artificial gravity on the cardiovascular system: Computational approach
NASA Astrophysics Data System (ADS)
Diaz Artiles, Ana; Heldt, Thomas; Young, Laurence R.
2016-09-01
steady-state cardiovascular behavior during sustained artificial gravity and exercise. Further validation of the model was performed using experimental data from the combined exercise and artificial gravity experiments conducted on the MIT CRC, and these results will be presented separately in future publications. This unique computational framework can be used to simulate a variety of centrifuge configuration and exercise intensities to improve understanding and inform decisions about future implementation of artificial gravity in space.
A new computer approach to mixed feature classification for forestry application
NASA Technical Reports Server (NTRS)
Kan, E. P.
1976-01-01
A computer approach for mapping mixed forest features (i.e., types, classes) from computer classification maps is discussed. Mixed features such as mixed softwood/hardwood stands are treated as admixtures of softwood and hardwood areas. Large-area mixed features are identified and small-area features neglected when the nominal size of a mixed feature can be specified. The computer program merges small isolated areas into surrounding areas by the iterative manipulation of the postprocessing algorithm that eliminates small connected sets. For a forestry application, computer-classified LANDSAT multispectral scanner data of the Sam Houston National Forest were used to demonstrate the proposed approach. The technique was successful in cleaning the salt-and-pepper appearance of multiclass classification maps and in mapping admixtures of softwood areas and hardwood areas. However, the computer-mapped mixed areas matched very poorly with the ground truth because of inadequate resolution and inappropriate definition of mixed features.
A scalable approach to modeling groundwater flow on massively parallel computers
Ashby, S.F.; Falgout, R.D.; Tompson, A.F.B.
1995-12-01
We describe a fully scalable approach to the simulation of groundwater flow on a hierarchy of computing platforms, ranging from workstations to massively parallel computers. Specifically, we advocate the use of scalable conceptual models in which the subsurface model is defined independently of the computational grid on which the simulation takes place. We also describe a scalable multigrid algorithm for computing the groundwater flow velocities. We axe thus able to leverage both the engineer`s time spent developing the conceptual model and the computing resources used in the numerical simulation. We have successfully employed this approach at the LLNL site, where we have run simulations ranging in size from just a few thousand spatial zones (on workstations) to more than eight million spatial zones (on the CRAY T3D)-all using the same conceptual model.
Filippi, Anthony M; Bhaduri, Budhendra L; Naughton, III, Thomas J; King, Amy L; Scott, Stephen L; Guneralp, Inci
2012-01-01
Abstract For aquatic studies, radiative transfer (RT) modeling can be used to compute hyperspectral above-surface remote sensing reflectance that can be utilized for inverse model development. Inverse models can provide bathymetry and inherent-and bottom-optical property estimation. Because measured oceanic field/organic datasets are often spatio-temporally sparse, synthetic data generation is useful in yielding sufficiently large datasets for inversion model development; however, these forward-modeled data are computationally expensive and time-consuming to generate. This study establishes the magnitude of wall-clock-time savings achieved for performing large, aquatic RT batch-runs using parallel computing versus a sequential approach. Given 2,600 simulations and identical compute-node characteristics, sequential architecture required ~100 hours until termination, whereas a parallel approach required only ~2.5 hours (42 compute nodes) a 40x speed-up. Tools developed for this parallel execution are discussed.
Fillippi, Anthony; Bhaduri, Budhendra L; Naughton, III, Thomas J; King, Amy L; Scott, Stephen L; Guneralp, Inci
2012-01-01
For aquatic studies, radiative transfer (RT) modeling can be used to compute hyperspectral above-surface remote sensing reflectance that can be utilized for inverse model development. Inverse models can provide bathymetry and inherent- and bottom-optical property estimation. Because measured oceanic field/organic datasets are often spatio-temporally sparse, synthetic data generation is useful in yielding sufficiently large datasets for inversion model development; however, these forward-modeled data are computationally expensive and time-consuming to generate. This study establishes the magnitude of wall-clock-time savings achieved for performing large, aquatic RT batch-runs using parallel computing versus a sequential approach. Given 2,600 simulations and identical compute-node characteristics, sequential architecture required {approx}100 hours until termination, whereas a parallel approach required only {approx}2.5 hours (42 compute nodes) - a 40x speed-up. Tools developed for this parallel execution are discussed.
Combined Experimental and Computational Approach to Predict the Glass-Water Reaction
Pierce, Eric M.; Bacon, Diana H.
2011-10-01
The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic timescales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models be validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year-long PUF experiment was conducted with the Subsurface Transport Over Reactive Multiphases (STORM) code. Results show that parameterization of the computer model by combining direct bench scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year-long test duration, the rate decreased from 0.2 to 0.01 g/(m2 day) based on B release for low-activity waste glass LAWA44. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by four orders of magnitude) and suggests that the gel-layer properties are less protective under these dynamic
Combined Experimental and Computational Approach to Predict the Glass-Water Reaction
Pierce, Eric M; Bacon, Diana
2011-01-01
The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic time-scales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models are validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases code. Results show that parameterization of the computer model by combining direct bench-scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year long test duration, the rate decreased from 0.2 to 0.01 g/(m2 d) base on B release. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by 4 orders of magnitude) and suggest the gel-layer properties are less protective under these dynamic conditions.
Glacial landscape evolution by subglacial quarrying: A multiscale computational approach
NASA Astrophysics Data System (ADS)
Ugelvig, Sofie V.; Egholm, David L.; Iverson, Neal R.
2016-11-01
Quarrying of bedrock is a primary agent of subglacial erosion. Although the mechanical theory behind the process has been studied for decades, it has proven difficult to formulate the governing principles so that large-scale landscape evolution models can be used to integrate erosion over time. The existing mechanical theory thus stands largely untested in its ability to explain postglacial topography. In this study we relate the physics of quarrying to long-term landscape evolution with a multiscale approach that connects meter-scale cavities to kilometer-scale glacial landscapes. By averaging the quarrying rate across many small-scale bedrock steps, we quantify how regional trends in basal sliding speed, effective pressure, and bed slope affect the rate of erosion. A sensitivity test indicates that a power law formulated in terms of these three variables provides an acceptable basis for quantifying regional-scale rates of quarrying. Our results highlight the strong influence of effective pressure, which intensifies quarrying by increasing the volume of the bed that is stressed by the ice and thereby the probability of rock failure. The resulting pressure dependency points to subglacial hydrology as a primary factor for influencing rates of quarrying and hence for shaping the bedrock topography under warm-based glaciers. When applied in a landscape evolution model, the erosion law for quarrying produces recognizable large-scale glacial landforms: U-shaped valleys, hanging valleys, and overdeepenings. The landforms produced are very similar to those predicted by more standard sliding-based erosion laws, but overall quarrying is more focused in valleys, and less effective at higher elevations.
2015-01-01
Technical Paper 3. DATES COVERED (From - To) January 2015-May 2015 4. TITLE AND SUBTITLE COMPUTATIONAL MODELING APPROACHES FOR STUDYING TRANSVERSE ...so that the effect of the transverse instability on the center study element can be examined parametrically. The second approach models the entire...APPROACHES FOR STUDYING TRANSVERSE COMBUSTION INSTABILITY IN A MULTI-ELEMENT INJECTOR M.E. Harvazinski1, K.J. Shipley2*, D.G. Talley1, V. Sankaran1, and
Management of low back pain in computer users: A multidisciplinary approach
Shete, Kiran M.; Suryawanshi, Prachi; Gandhi, Neha
2012-01-01
Background: Low back pain is a very common phenomenon in computer users. More than 80% people using computers for more than 4 h complain of back pain. Objective: To compare the effectiveness of multidisciplinary treatment approach and conventional treatment approach amongst computer users. Materials and Methods: A prospective interventional study was carried out at a private spine clinic amongst the computer users with the complaint of low back pain. The study participants were randomly distributed in two groups. The first group comprised the study participants treated by conventional approach and the second group was treated by multidisciplinary approach. Primary outcomes analyzed were pain intensity, sick leave availed, and quality of life. Statistical analysis was done using proportions, unpaired “t” test, and Wilcoxon signed-rank test. Results: Totally 44 study participants were randomly assigned to groups I and II, and each group had 22 study participants. Intensity of pain was reduced significantly in the group treated by multidisciplinary approach (t = 5.718; P = 0.0001). Similarly only 4 (19.19%) of the study participants of the group treated by multidisciplinary approach availed sick leave due to low back pain, while 14 (63.63%) study participants availed sick leave in the other group (P = 0.02). The quality of life amongst the study participants treated by multidisciplinary approach was significantly improved compared to the group treated by conventional approach (t = 7.037; P = 0.0001). Conclusion and Recommendation: The multidisciplinary treatment approach was better than the conventional treatment approach in low back pain cases when some factors like pain and quality of life were assessed. The multidisciplinary approach for treatment of low back pain should be promoted over conventional approach. Larger studies are required to confirm the findings in different settings. PMID:23741122
NASA Astrophysics Data System (ADS)
Merced-Grafals, Emmanuelle J.; Dávila, Noraica; Ge, Ning; Williams, R. Stanley; Strachan, John Paul
2016-09-01
Beyond use as high density non-volatile memories, memristors have potential as synaptic components of neuromorphic systems. We investigated the suitability of tantalum oxide (TaOx) transistor-memristor (1T1R) arrays for such applications, particularly the ability to accurately, repeatedly, and rapidly reach arbitrary conductance states. Programming is performed by applying an adaptive pulsed algorithm that utilizes the transistor gate voltage to control the SET switching operation and increase programming speed of the 1T1R cells. We show the capability of programming 64 conductance levels with <0.5% average accuracy using 100 ns pulses and studied the trade-offs between programming speed and programming error. The algorithm is also utilized to program 16 conductance levels on a population of cells in the 1T1R array showing robustness to cell-to-cell variability. In general, the proposed algorithm results in approximately 10× improvement in programming speed over standard algorithms that do not use the transistor gate to control memristor switching. In addition, after only two programming pulses (an initialization pulse followed by a programming pulse), the resulting conductance values are within 12% of the target values in all cases. Finally, endurance of more than 106 cycles is shown through open-loop (single pulses) programming across multiple conductance levels using the optimized gate voltage of the transistor. These results are relevant for applications that require high speed, accurate, and repeatable programming of the cells such as in neural networks and analog data processing.
Accurate quantum chemical calculations
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.
Merced-Grafals, Emmanuelle J; Dávila, Noraica; Ge, Ning; Williams, R Stanley; Strachan, John Paul
2016-09-09
Beyond use as high density non-volatile memories, memristors have potential as synaptic components of neuromorphic systems. We investigated the suitability of tantalum oxide (TaOx) transistor-memristor (1T1R) arrays for such applications, particularly the ability to accurately, repeatedly, and rapidly reach arbitrary conductance states. Programming is performed by applying an adaptive pulsed algorithm that utilizes the transistor gate voltage to control the SET switching operation and increase programming speed of the 1T1R cells. We show the capability of programming 64 conductance levels with <0.5% average accuracy using 100 ns pulses and studied the trade-offs between programming speed and programming error. The algorithm is also utilized to program 16 conductance levels on a population of cells in the 1T1R array showing robustness to cell-to-cell variability. In general, the proposed algorithm results in approximately 10× improvement in programming speed over standard algorithms that do not use the transistor gate to control memristor switching. In addition, after only two programming pulses (an initialization pulse followed by a programming pulse), the resulting conductance values are within 12% of the target values in all cases. Finally, endurance of more than 10(6) cycles is shown through open-loop (single pulses) programming across multiple conductance levels using the optimized gate voltage of the transistor. These results are relevant for applications that require high speed, accurate, and repeatable programming of the cells such as in neural networks and analog data processing.
NASA Technical Reports Server (NTRS)
Fleming, M. D.; Berkebile, J. S.; Hoffer, R. M.
1975-01-01
Three approaches for analyzing Landsat-1 data from Ludwig Mountain in the San Juan Mountain range in Colorado are considered. In the 'supervised' approach the analyst selects areas of known spectral cover types and specifies these to the computer as training fields. Statistics are obtained for each cover type category and the data are classified. Such classifications are called 'supervised' because the analyst has defined specific areas of known cover types. The second approach uses a clustering algorithm which divides the entire training area into a number of spectrally distinct classes. Because the analyst need not define particular portions of the data for use but has only to specify the number of spectral classes into which the data is to be divided, this classification is called 'nonsupervised'. A hybrid method which selects training areas of known cover type but then uses the clustering algorithm to refine the data into a number of unimodal spectral classes is called the 'modified-supervised' approach.
Computational approaches for ligand discovery and design in class-A G protein- coupled receptors.
Rodríguez, David; Gutiérrez-de-Terán, Hugo
2013-01-01
Our structural understanding of the superfamily of G-protein coupled receptors, a group of targets of utmost pharmacological importance, has improved dramatically in the last few years. This was directly translated in an increase of both the number and the relevance of computer-assisted drug design efforts devoted to these receptors. The field, which had been greatly influenced by ligand-based methods, has experienced a radical transformation with a number of successful structure-based ligand design and ligand discovery studies. This revolution has been accompanied by the exponential increase of computational resources, and as a result the scenario in GPCR structural and chemical studies is now more complex and richer than ever. Virtual screens, both structure- and ligand-based, co-exist with accurate computational characterizations of the receptor conformational dynamics and of the energy landscapes of receptor-ligand interactions. We here provide an integrated and updated view of the different computational techniques applied to the ligand design of GPCRs. Particular emphasis is put on the studies that take into account the novel structural information of GPCRs, together with those that consider the enormous amount of chemical information accumulated on these receptors in the last decades. Indeed, we propose that proper combinations of the different computational techniques: ligand-based, structure-based and molecular dynamics studies, should be performed to better integrate all available information whenever possible. With this in mind, a major impact of computational technologies in the ligand design on GPCRs is expected in the forthcoming years.
Non-invasive computation of aortic pressure maps: a phantom-based study of two approaches
NASA Astrophysics Data System (ADS)
Delles, Michael; Schalck, Sebastian; Chassein, Yves; Müller, Tobias; Rengier, Fabian; Speidel, Stefanie; von Tengg-Kobligk, Hendrik; Kauczor, Hans-Ulrich; Dillmann, Rüdiger; Unterhinninghofen, Roland
2014-03-01
Patient-specific blood pressure values in the human aorta are an important parameter in the management of cardiovascular diseases. A direct measurement of these values is only possible by invasive catheterization at a limited number of measurement sites. To overcome these drawbacks, two non-invasive approaches of computing patient-specific relative aortic blood pressure maps throughout the entire aortic vessel volume are investigated by our group. The first approach uses computations from complete time-resolved, three-dimensional flow velocity fields acquired by phasecontrast magnetic resonance imaging (PC-MRI), whereas the second approach relies on computational fluid dynamics (CFD) simulations with ultrasound-based boundary conditions. A detailed evaluation of these computational methods under realistic conditions is necessary in order to investigate their overall robustness and accuracy as well as their sensitivity to certain algorithmic parameters. We present a comparative study of the two blood pressure computation methods in an experimental phantom setup, which mimics a simplified thoracic aorta. The comparative analysis includes the investigation of the impact of algorithmic parameters on the MRI-based blood pressure computation and the impact of extracting pressure maps in a voxel grid from the CFD simulations. Overall, a very good agreement between the results of the two computational approaches can be observed despite the fact that both methods used completely separate measurements as input data. Therefore, the comparative study of the presented work indicates that both non-invasive pressure computation methods show an excellent robustness and accuracy and can therefore be used for research purposes in the management of cardiovascular diseases.
Qiu, Peng; Gentles, Andrew J; Plevritis, Sylvia K
2010-02-01
Information theoretic approaches are increasingly being used for reconstructing regulatory networks from microarray data. These approaches start by computing the pairwise mutual information (MI) between all gene pairs. The resulting MI matrix is then manipulated to identify regulatory relationships. A barrier to these approaches is the time-consuming step of computing the MI matrix. We present a method to reduce this computation time. We apply spectral analysis to re-order the genes, so that genes that share regulatory relationships are more likely to be placed close to each other. Then, using a "sliding window" approach with appropriate window size and step size, we compute the MI for the genes within the sliding window, and the remainder is assumed to be zero. Using both simulated data and microarray data, we demonstrate that our method does not incur performance loss in regions of high-precision and low-recall, while the computational time is significantly lowered. The proposed method can be used with any method that relies on the mutual information to reconstruct networks.
An Approach to Integrate a Space-Time GIS Data Model with High Performance Computers
Wang, Dali; Zhao, Ziliang; Shaw, Shih-Lung
2011-01-01
In this paper, we describe an approach to integrate a Space-Time GIS data model on a high performance computing platform. The Space-Time GIS data model has been developed on a desktop computing environment. We use the Space-Time GIS data model to generate GIS module, which organizes a series of remote sensing data. We are in the process of porting the GIS module into an HPC environment, in which the GIS modules handle large dataset directly via parallel file system. Although it is an ongoing project, authors hope this effort can inspire further discussions on the integration of GIS on high performance computing platforms.
ERIC Educational Resources Information Center
Castleman, Jacquelyn B.
This practicum was designed to lessen the computer anxiety of early childhood education majors enrolled in General Curriculum or General Methods courses, to assist them in learning more about computer applications, and to increase the amount of time spent using computers. Weekly guidelines were given to the students, and a hands-on approach was…
ERIC Educational Resources Information Center
Wang, Chu-Fu; Lin, Chih-Lung; Deng, Jien-Han
2012-01-01
Testing is an important stage of teaching as it can assist teachers in auditing students' learning results. A good test is able to accurately reflect the capability of a learner. Nowadays, Computer-Assisted Testing (CAT) is greatly improving traditional testing, since computers can automatically and quickly compose a proper test sheet to meet user…
Aberg, Kristoffer Carl; Doell, Kimberly C; Schwartz, Sophie
2016-01-01
Learning how to gain rewards (approach learning) and avoid punishments (avoidance learning) is fundamental for everyday life. While individual differences in approach and avoidance learning styles have been related to genetics and aging, the contribution of personality factors, such as traits, remains undetermined. Moreover, little is known about the computational mechanisms mediating differences in learning styles. Here, we used a probabilistic selection task with positive and negative feedbacks, in combination with computational modelling, to show that individuals displaying better approach (vs. avoidance) learning scored higher on measures of approach (vs. avoidance) trait motivation, but, paradoxically, also displayed reduced learning speed following positive (vs. negative) outcomes. These data suggest that learning different types of information depend on associated reward values and internal motivational drives, possibly determined by personality traits.
Carl Aberg, Kristoffer; Doell, Kimberly C.; Schwartz, Sophie
2016-01-01
Learning how to gain rewards (approach learning) and avoid punishments (avoidance learning) is fundamental for everyday life. While individual differences in approach and avoidance learning styles have been related to genetics and aging, the contribution of personality factors, such as traits, remains undetermined. Moreover, little is known about the computational mechanisms mediating differences in learning styles. Here, we used a probabilistic selection task with positive and negative feedbacks, in combination with computational modelling, to show that individuals displaying better approach (vs. avoidance) learning scored higher on measures of approach (vs. avoidance) trait motivation, but, paradoxically, also displayed reduced learning speed following positive (vs. negative) outcomes. These data suggest that learning different types of information depend on associated reward values and internal motivational drives, possibly determined by personality traits. PMID:27851807
An approach to experimental evaluation of real-time fault-tolerant distributed computing schemes
NASA Technical Reports Server (NTRS)
Kim, K. H.
1989-01-01
A testbed-based approach to the evaluation of fault-tolerant distributed computing schemes is discussed. The approach is based on experimental incorporation of system structuring and design techniques into real-time distributed-computing testbeds centered around tightly coupled microcomputer networks. The effectiveness of this approach has been experimentally confirmed. Primary advantages of this approach include the accuracy of the timing and logical-complexity data and the degree of assurance of the practical effectiveness of the scheme evaluated. Various design issues encountered in the course of establishing the network testbed facilities are discussed, along with their augmentation to support some experiments. The shortcomings of the testbeds are also discussed together with the desired extensions of the testbeds.
2010-04-14
novel methods for discretization based on Legendre-Gauss and Legendre-Gauss- Radau quadrature points. Using this approach, the finite-dimensional...Gauss- Radau quadrature points. Using this approach, the finite-dimensional approximation is kept low-dimensional, potentially enabling near real...Costate Estimation of Finite-Horizon and Infinite-Horizon Optimal Control Problems Using a Radau Pseudospectral Method,” Computational Optimization and
2015-05-01
Charts 3. DATES COVERED (From - To) May 2015- June 2015 4. TITLE AND SUBTITLE COMPUTATIONAL MODELING APPROACHES FOR STUDYING TRANSVERSE COMBUSTION...an artificial forcing term. The forcing amplitude can be adjusted so that the effect of the transverse instability on the center study element can be...Approaches for Studying Transverse Combustion Instability in a Multi-element Injector Matt Harvazinski1, Kevin Shipley2, Doug Talley1, Venke Sankaran1
Lan, Yu; Zou, Lufeng; Cao, Yang; Houk, K N
2011-12-01
Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.
Belge, Bénédicte; Coche, Emmanuel; Pasquet, Agnès; Vanoverschelde, Jean-Louis J; Gerber, Bernhard L
2006-07-01
Retrospective reconstruction of ECG-gated images at different parts of the cardiac cycle allows the assessment of cardiac function by multi-detector row CT (MDCT) at the time of non-invasive coronary imaging. We compared the accuracy of such measurements by MDCT to cine magnetic resonance (MR). Forty patients underwent the assessment of global and regional cardiac function by 16-slice MDCT and cine MR. Left ventricular (LV) end-diastolic and end-systolic volumes estimated by MDCT (134+/-51 and 67+/-56 ml) were similar to those by MR (137+/-57 and 70+/-60 ml, respectively; both P=NS) and strongly correlated (r=0.92 and r=0.95, respectively; both P<0.001). Consequently, LV ejection fractions by MDCT and MR were also similar (55+/-21 vs. 56+/-21%; P=NS) and highly correlated (r=0.95; P<0.001). Regional end-diastolic and end-systolic wall thicknesses by MDCT were highly correlated (r=0.84 and r=0.92, respectively; both P<0.001), but significantly lower than by MR (8.3+/-1.8 vs. 8.8+/-1.9 mm and 12.7+/-3.4 vs. 13.3+/-3.5 mm, respectively; both P<0.001). Values of regional wall thickening by MDCT and MR were similar (54+/-30 vs. 51+/-31%; P=NS) and also correlated well (r=0.91; P<0.001). Retrospectively gated MDCT can accurately estimate LV volumes, EF and regional LV wall thickening compared to cine MR.
NASA Astrophysics Data System (ADS)
Fazanaro, Filipe I.; Soriano, Diogo C.; Suyama, Ricardo; Madrid, Marconi K.; Oliveira, José Raimundo de; Muñoz, Ignacio Bravo; Attux, Romis
2016-08-01
The characterization of nonlinear dynamical systems and their attractors in terms of invariant measures, basins of attractions and the structure of their vector fields usually outlines a task strongly related to the underlying computational cost. In this work, the practical aspects related to the use of parallel computing - specially the use of Graphics Processing Units (GPUS) and of the Compute Unified Device Architecture (CUDA) - are reviewed and discussed in the context of nonlinear dynamical systems characterization. In this work such characterization is performed by obtaining both local and global Lyapunov exponents for the classical forced Duffing oscillator. The local divergence measure was employed by the computation of the Lagrangian Coherent Structures (LCSS), revealing the general organization of the flow according to the obtained separatrices, while the global Lyapunov exponents were used to characterize the attractors obtained under one or more bifurcation parameters. These simulation sets also illustrate the required computation time and speedup gains provided by different parallel computing strategies, justifying the employment and the relevance of GPUS and CUDA in such extensive numerical approach. Finally, more than simply providing an overview supported by a representative set of simulations, this work also aims to be a unified introduction to the use of the mentioned parallel computing tools in the context of nonlinear dynamical systems, providing codes and examples to be executed in MATLAB and using the CUDA environment, something that is usually fragmented in different scientific communities and restricted to specialists on parallel computing strategies.
Monte Carlo Computation of the Finite-Size Scaling Function: an Alternative Approach
NASA Astrophysics Data System (ADS)
Kim, Jae-Kwon; de Souza, Adauto J. F.; Landau, D. P.
1996-03-01
We show how to compute numerically a finite-size-scaling function which is particularly effective in extracting accurate infinite- volume -limit values (bulk values) of certain physical quantities^1. We illustrate our procedure for the two and three dimensional Ising models, and report our bulk values for the correlation lenth, magnetic susceptibility, and renormalized four-point coupling constant. Based on these bulk values we extract the values of various critical parameters. ^1 J.-K. Kim, Euro. Phys. Lett. 28, 211 (1994) Research supported in part by the NSF ^Permanent address: Departmento de Fisica e Matematica, Universidade Federal Rural de Pernambuco, 52171-900, Recife, Pernambuco, Brazil
A dual-energy approach for improvement of the measurement consistency in computed tomography
NASA Astrophysics Data System (ADS)
Jansson, Anton; Pejryd, Lars
2016-11-01
Computed tomography is increasingly adopted by industries for metrological and material evaluation. The technology enables new measurement possibilities, while also challenging old measurement methods in their established territories. There are, however, uncertainties related with the computed tomography method. Investigation of multi-material components with, in particular, varying material thickness can result in unreliable measurements. In this paper the effects of multi-materials, and differing material thickness, on computed tomography measurement consistency has been studied. The aim of the study was to identify measurement inconsistencies and attempt to correct these with a dual-energy computed tomography approach. In this pursuit, a multi-material phantom was developed, containing reliable measurement points and custom-ability with regards to material combinations. A dual-energy method was developed and implemented using sequential acquisition and pre-reconstruction fusing of projections. It was found that measurements made on the multi-material phantom with a single computed tomography scan were highly inconsistent. It was also found that the dual-energy approach was able to reduce the measurement inconsistencies. However, more work is required with the automation of the dual-energy approach presented in this paper since it is highly operator dependant.
ERIC Educational Resources Information Center
Yeh, Duen-Yian; Cheng, Ching-Hsue
2016-01-01
This study examined the relationships among children's computer game use, academic achievement and parental governing approach to propose probable answers for the doubts of Taiwanese parents. 355 children (ages 11-14) were randomly sampled from 20 elementary schools in a typically urbanised county in Taiwan. Questionnaire survey (five questions)…
The Computational Experiment and Its Effects on Approach to Learning and Beliefs on Physics
ERIC Educational Resources Information Center
Psycharis, Sarantos
2011-01-01
Contemporary instructional approaches expect students to be active producers of knowledge. This leads to the need for creation of instructional tools and tasks that can offer students opportunities for active learning. This study examines the effect of a computational experiment as an instructional tool-for Grade 12 students, using a computer…
Laplace transform approach for solving integral equations using computer algebra system
NASA Astrophysics Data System (ADS)
Paneva-Konovska, Jordanka; Nikolova, Yanka
2016-12-01
The Laplace transform method, along with Computer Algebra Systems (CAS) "Maple" v. 13, are extremely successfully applied for solving a class of integral equations with an arbitrary order, including fractional order integral equations. The combining of both powerful approaches allows students more quickly, enjoyable and thoroughly to master the material.
Benson, W.H., R.T. Di Giulio, J.C. Cook, J. Freedman, R.L. Malek, C. Thompson and D. Versteeg. In press. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary Report (Abstract). To be presented at the SETAC Fourth World Congress, 14-...
The Criterion-Related Validity of a Computer-Based Approach for Scoring Concept Maps
ERIC Educational Resources Information Center
Clariana, Roy B.; Koul, Ravinder; Salehi, Roya
2006-01-01
This investigation seeks to confirm a computer-based approach that can be used to score concept maps (Poindexter & Clariana, 2004) and then describes the concurrent criterion-related validity of these scores. Participants enrolled in two graduate courses (n=24) were asked to read about and research online the structure and function of the heart…
A "Black-and-White Box" Approach to User Empowerment with Component Computing
ERIC Educational Resources Information Center
Kynigos, C.
2004-01-01
The paper discusses three aspects central to the 10 year-old process of design, development and use of E-slate, a construction kit for educational software. These are: (1) the design of computational media for user empowerment, (2) the socially-grounded approach to the building of user communities and (3) the issue of long-term sustainability as…
An Integrated Approach to Teaching Students the Use of Computers in Science.
ERIC Educational Resources Information Center
Hood, B. James
1991-01-01
Reported is an approach to teaching the use of Macintosh computers to sixth, seventh, and eighth grade students within the context of a simplified model of scientific research including proposal, data collection and analyses, and presentation of findings. Word processing, graphing, statistical, painting, and poster software were sequentially…
A Computer-Assisted Multiliteracies Programme as an Alternative Approach to EFL Instruction
ERIC Educational Resources Information Center
Lee, Kyungmee; Ardeshiri, Minoo; Cummins, Jim
2016-01-01
The aim of this article is to introduce a computer-assisted multiliteracies programme (CaMP) as an alternative approach to English as a Foreign Language (EFL) instruction in order to overcome the educational limitations that are inherent in most EFL settings. In a number of monolingual societies with a dominant language other than English,…
The Effects of Computer Supported Problem Based Learning on Students' Approaches to Learning
ERIC Educational Resources Information Center
Ak, Serife
2011-01-01
The purpose of this paper is to investigate the effects of computer supported problem based learning on students' approaches to learning. The research was conducted as a pre-test and posttest one-grouped design used to achieve the objectives of the study. The experimental process of study lasted 5 weeks and was carried out on 78 university…
A Computer-Based Spatial Learning Strategy Approach That Improves Reading Comprehension and Writing
ERIC Educational Resources Information Center
Ponce, Hector R.; Mayer, Richard E.; Lopez, Mario J.
2013-01-01
This article explores the effectiveness of a computer-based spatial learning strategy approach for improving reading comprehension and writing. In reading comprehension, students received scaffolded practice in translating passages into graphic organizers. In writing, students received scaffolded practice in planning to write by filling in graphic…
Learning Probabilities in Computer Engineering by Using a Competency- and Problem-Based Approach
ERIC Educational Resources Information Center
Khoumsi, Ahmed; Hadjou, Brahim
2005-01-01
Our department has redesigned its electrical and computer engineering programs by adopting a learning methodology based on competence development, problem solving, and the realization of design projects. In this article, we show how this pedagogical approach has been successfully used for learning probabilities and their application to computer…
WPS mediation: An approach to process geospatial data on different computing backends
NASA Astrophysics Data System (ADS)
Giuliani, Gregory; Nativi, Stefano; Lehmann, Anthony; Ray, Nicolas
2012-10-01
The OGC Web Processing Service (WPS) specification allows generating information by processing distributed geospatial data made available through Spatial Data Infrastructures (SDIs). However, current SDIs have limited analytical capacities and various problems emerge when trying to use them in data and computing-intensive domains such as environmental sciences. These problems are usually not or only partially solvable using single computing resources. Therefore, the Geographic Information (GI) community is trying to benefit from the superior storage and computing capabilities offered by distributed computing (e.g., Grids, Clouds) related methods and technologies. Currently, there is no commonly agreed approach to grid-enable WPS. No implementation allows one to seamlessly execute a geoprocessing calculation following user requirements on different computing backends, ranging from a stand-alone GIS server up to computer clusters and large Grid infrastructures. Considering this issue, this paper presents a proof of concept by mediating different geospatial and Grid software packages, and by proposing an extension of WPS specification through two optional parameters. The applicability of this approach will be demonstrated using a Normalized Difference Vegetation Index (NDVI) mediated WPS process, highlighting benefits, and issues that need to be further investigated to improve performances.
NASA Technical Reports Server (NTRS)
Bey, K. S.; Thornton, E. A.; Dechaumphai, P.; Ramakrishnan, R.
1985-01-01
Recent progress in the development of finite element methodology for the prediction of aerothermal loads is described. Two dimensional, inviscid computations are presented, but emphasis is placed on development of an approach extendable to three dimensional viscous flows. Research progress is described for: (1) utilization of a commercially available program to construct flow solution domains and display computational results, (2) development of an explicit Taylor-Galerkin solution algorithm, (3) closed form evaluation of finite element matrices, (4) vector computer programming strategies, and (5) validation of solutions. Two test problems of interest to NASA Langley aerothermal research are studied. Comparisons of finite element solutions for Mach 6 flow with other solution methods and experimental data validate fundamental capabilities of the approach for analyzing high speed inviscid compressible flows.
NASA Technical Reports Server (NTRS)
Bey, K. S.; Thornton, E. A.; Dechaumphai, P.; Ramakrishnan, R.
1985-01-01
Recent progress in the development of finite element methodology for the prediction of aerothermal loads is described. Two dimensional, inviscid computations are presented, but emphasis is placed on development of an approach extendable to three dimensional viscous flows. Research progress is described for: (1) utilization of a commerically available program to construct flow solution domains and display computational results, (2) development of an explicit Taylor-Galerkin solution algorithm, (3) closed form evaluation of finite element matrices, (4) vector computer programming strategies, and (5) validation of solutions. Two test problems of interest to NASA Langley aerothermal research are studied. Comparisons of finite element solutions for Mach 6 flow with other solution methods and experimental data validate fundamental capabilities of the approach for analyzing high speed inviscid compressible flows.
A new computational approach for modeling diffusion tractography in the brain
Garimella, Harsha T.; Kraft, Reuben H.
2017-01-01
Computational models provide additional tools for studying the brain, however, many techniques are currently disconnected from each other. There is a need for new computational approaches that span the range of physics operating in the brain. In this review paper, we offer some new perspectives on how the embedded element method can fill this gap and has the potential to connect a myriad of modeling genre. The embedded element method is a mesh superposition technique used within finite element analysis. This method allows for the incorporation of axonal fiber tracts to be explicitly represented. Here, we explore the use of the approach beyond its original goal of predicting axonal strain in brain injury. We explore the potential application of the embedded element method in areas of electrophysiology, neurodegeneration, neuropharmacology and mechanobiology. We conclude that this method has the potential to provide us with an integrated computational framework that can assist in developing improved diagnostic tools and regeneration technologies. PMID:28250733
A new computational approach for modeling diffusion tractography in the brain.
Garimella, Harsha T; Kraft, Reuben H
2017-01-01
Computational models provide additional tools for studying the brain, however, many techniques are currently disconnected from each other. There is a need for new computational approaches that span the range of physics operating in the brain. In this review paper, we offer some new perspectives on how the embedded element method can fill this gap and has the potential to connect a myriad of modeling genre. The embedded element method is a mesh superposition technique used within finite element analysis. This method allows for the incorporation of axonal fiber tracts to be explicitly represented. Here, we explore the use of the approach beyond its original goal of predicting axonal strain in brain injury. We explore the potential application of the embedded element method in areas of electrophysiology, neurodegeneration, neuropharmacology and mechanobiology. We conclude that this method has the potential to provide us with an integrated computational framework that can assist in developing improved diagnostic tools and regeneration technologies.
Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding.
Montalvo-Acosta, Joel José; Cecchini, Marco
2016-12-01
The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline.
NASA Astrophysics Data System (ADS)
Carelli, Fabio; Gianturco, Francesco Antonio
2016-06-01
The interaction of low-energy scattering electrons/positrons with molecular targets characterized by a "supercritical" permanent dipole moment (≳2.0 D) presents special physical characteristics that affect their spatial distributions, around the nuclear network of the molecular partners, both above and below the energy thresholds. Such special states are described as either dipole scattering states (DSS) above thresholds or as dipole bound states (DBS) below thresholds. The details of their respective behaviour will be presented and discussed in this work in the case of the purinic DNA bases of adenine and guanine. The behavior of the additional electron, in particular, will be discussed in detail by providing new computational results that will be related to the findings from recent experiments on the same DNA bases, confirming the transient electron's behaviour surmised by them. This work is affectionately dedicated to Michael Allan on the occasion of his official retirement. We wish to this dear friend and outstanding scientist many years to come in the happy pursuit of his many scientific interests.Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.
A comparative approach to computer aided design model of a dog femur.
Turamanlar, O; Verim, O; Karabulut, A
2016-01-01
Computer assisted technologies offer new opportunities in medical imaging and rapid prototyping in biomechanical engineering. Three dimensional (3D) modelling of soft tissues and bones are becoming more important. The accuracy of the analysis in modelling processes depends on the outline of the tissues derived from medical images. The aim of this study is the evaluation of the accuracy of 3D models of a dog femur derived from computed tomography data by using point cloud method and boundary line method on several modelling software. Solidworks, Rapidform and 3DSMax software were used to create 3D models and outcomes were evaluated statistically. The most accurate 3D prototype of the dog femur was created with stereolithography method using rapid prototype device. Furthermore, the linearity of the volumes of models was investigated between software and the constructed models. The difference between the software and real models manifests the sensitivity of the software and the devices used in this manner.
Redlarski, Grzegorz; Jaworski, Jacek
2013-10-01
This paper presents a new versatile approach to model severe human respiratory diseases via computer simulation. The proposed approach enables one to predict the time histories of various diseases via information accessible in medical publications. This knowledge is useful to bioengineers involved in the design and construction of medical devices that are employed for monitoring of respiratory condition. The approach provides the data that are crucial for testing diagnostic systems. This can be achieved without the necessity of probing the physiological details of the respiratory system as well as without identification of parameters that are based on measurement data.
Toward Accurate and Quantitative Comparative Metagenomics
Nayfach, Stephen; Pollard, Katherine S.
2016-01-01
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341
NASA Technical Reports Server (NTRS)
Drake, Jeffrey T.; Prasad, Nadipuram R.
1999-01-01
This paper surveys recent advances in communications that utilize soft computing approaches to phase synchronization. Soft computing, as opposed to hard computing, is a collection of complementary methodologies that act in producing the most desirable control, decision, or estimation strategies. Recently, the communications area has explored the use of the principal constituents of soft computing, namely, fuzzy logic, neural networks, and genetic algorithms, for modeling, control, and most recently for the estimation of phase in phase-coherent communications. If the receiver in a digital communications system is phase-coherent, as is often the case, phase synchronization is required. Synchronization thus requires estimation and/or control at the receiver of an unknown or random phase offset.
Examination of computer task exposures in radiologists: a work systems approach.
Robertson, Michelle M; Boiselle, Philip; Eisenberg, Ronald; Siegal, Dainel; Chang, Che-Hsu Joe; Dainoff, Marvin; Garabet, Angela; Garza, Jennifer Bruno; Dennerlein, Jack
2012-01-01
Radiologists are intensive computer users as they review and interpret radiological examinations using the Picture Archiving and Communication Systems (PACS). Since their computer tasks require the prolonged use of pointing devices, a high prevalence of Musculoskeletal Disorders (MSDs) is reported. The first phase of this study involved conducting a Cognitive Work Analysis in conjunction with a Participatory Ergonomics approach to perform a total work system analysis. We also conducted an ergonomic survey as well as collected computer use data, specifically for the mouse and keyboard. The goal of the study was to reduce the physical exposures for radiologists. This paper presents Phase I results describing the analyses and redesign process of the radiologists tasks, training design, computer use, and selected survey results.
A computationally efficient approach for hidden-Markov model-augmented fingerprint-based positioning
NASA Astrophysics Data System (ADS)
Roth, John; Tummala, Murali; McEachen, John
2016-09-01
This paper presents a computationally efficient approach for mobile subscriber position estimation in wireless networks. A method of data scaling assisted by timing adjust is introduced in fingerprint-based location estimation under a framework which allows for minimising computational cost. The proposed method maintains a comparable level of accuracy to the traditional case where no data scaling is used and is evaluated in a simulated environment under varying channel conditions. The proposed scheme is studied when it is augmented by a hidden-Markov model to match the internal parameters to the channel conditions that present, thus minimising computational cost while maximising accuracy. Furthermore, the timing adjust quantity, available in modern wireless signalling messages, is shown to be able to further reduce computational cost and increase accuracy when available. The results may be seen as a significant step towards integrating advanced position-based modelling with power-sensitive mobile devices.
Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim
2016-01-01
Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192
Lopez, Peter P; Cohn, Stephen M; Popkin, Charles A; Jackowski, Julie; Michalek, Joel E
2007-12-01
Diagnosing appendicitis continues to be a difficult task for clinicians. The use of routine CT scan has been advocated to improve the accuracy of diagnosing appendicitis. When compared with the use of clinical examination alone, CT scan was not significantly different with regard to making the diagnosis of appendicitis in women of childbearing age. The use of computed tomography in making the diagnosis of appendicitis has become the current standard of practice in most emergency rooms. In women of childbearing age, with possible appendicitis, we prospectively compared clinical observation alone (OBS) to appendiceal CT scan with clinical observation (CT). Ninety women (OBS: 48, CT: 42) with questionable appendicitis and an Alvarado Score ranging from two to eight were prospectively randomized. A true positive study/exam resulted in a laparotomy that revealed a lesion requiring operation (confirmed by pathology). A true negative exam/study did not require operation. Hospital stay (OBS = 1.9 +/- 1.6 vs CT = 1.3 +/- 1.4 days) and charges (OBS = $9,459 +/- 7,358 vs CT = $9,443 +/- 8,773) were similar. The OBS group had an accuracy of 93 per cent, sensitivity of 100 per cent, and a specificity of 87.5 per cent. The CT group had an accuracy of 93 per cent, sensitivity of 89.5 per cent, and specificity of 95.6 per cent. Although this study is too small to statistically establish equivalence, the data suggest that a CT scan reliably identifies women who need an operation for appendicitis and seems to be as good as clinical examination.
Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z
2015-01-01
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.
Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.
2015-01-01
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260
Equation-Free Effective Computation for Discrete Systems: a Time Stepper Based Approach
NASA Astrophysics Data System (ADS)
Möller, J.; Runborg, O.; Kevrekidis, P. G.; Lust, K.; Kevrekidis, I. G.
We propose a computer-assisted approach to studying the effective continuum behavior of spatially discrete evolution equations. The advantage of the approach is that the "coarse model" (the continuum, effective equation) need not be explicitly constructed. The method only uses a time-integration code for the discrete problem and judicious choices of initial data and integration times; our bifurcation computations are based on the so-called Recursive Projection Method (RPM) with arc-length continuation [Shroff & Keller, 1993]. The technique is used to monitor features of the genuinely discrete problem such as the pinning of coherent structures and its results are compared to quasi-continuum approaches such as the ones based on Padé approximations.
A computational approach to continuum damping of Alfven waves in two and three-dimensional geometry
Koenies, Axel; Kleiber, Ralf
2012-12-15
While the usual way of calculating continuum damping of global Alfven modes is the introduction of a small artificial resistivity, we present a computational approach to the problem based on a suitable path of integration in the complex plane. This approach is implemented by the Riccati shooting method and it is shown that it can be transferred to the Galerkin method used in three-dimensional ideal magneto-hydrodynamics (MHD) codes. The new approach turns out to be less expensive with respect to resolution and computation time than the usual one. We present an application to large aspect ratio tokamak and stellarator equilibria retaining a few Fourier harmonics only and calculate eigenfunctions and continuum damping rates. These may serve as an input for kinetic MHD hybrid models making it possible to bypass the problem of having singularities on the path of integration on one hand and considering continuum damping on the other.
Sparse and accurate high resolution SAR imaging
NASA Astrophysics Data System (ADS)
Vu, Duc; Zhao, Kexin; Rowe, William; Li, Jian
2012-05-01
We investigate the usage of an adaptive method, the Iterative Adaptive Approach (IAA), in combination with a maximum a posteriori (MAP) estimate to reconstruct high resolution SAR images that are both sparse and accurate. IAA is a nonparametric weighted least squares algorithm that is robust and user parameter-free. IAA has been shown to reconstruct SAR images with excellent side lobes suppression and high resolution enhancement. We first reconstruct the SAR images using IAA, and then we enforce sparsity by using MAP with a sparsity inducing prior. By coupling these two methods, we can produce a sparse and accurate high resolution image that are conducive for feature extractions and target classification applications. In addition, we show how IAA can be made computationally efficient without sacrificing accuracies, a desirable property for SAR applications where the size of the problems is quite large. We demonstrate the success of our approach using the Air Force Research Lab's "Gotcha Volumetric SAR Data Set Version 1.0" challenge dataset. Via the widely used FFT, individual vehicles contained in the scene are barely recognizable due to the poor resolution and high side lobe nature of FFT. However with our approach clear edges, boundaries, and textures of the vehicles are obtained.
Accurate basis set truncation for wavefunction embedding
NASA Astrophysics Data System (ADS)
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
Frisby, Joshua; Smith, Vernon; Traub, Stephen; Patel, Vimla L
2017-01-01
Hospital Emergency Departments (EDs) frequently experience crowding. One of the factors that contributes to this crowding is the "door to doctor time", which is the time from a patient's registration to when the patient is first seen by a physician. This is also one of the Meaningful Use (MU) performance measures that emergency departments report to the Center for Medicare and Medicaid Services (CMS). Current documentation methods for this measure are inaccurate due to the imprecision in manual data collection. We describe a method for automatically (in real time) and more accurately documenting the door to physician time. Using sensor-based technology, the distance between the physician and the computer is calculated by using the single board computers installed in patient rooms that log each time a Bluetooth signal is seen from a device that the physicians carry. This distance is compared automatically with the accepted room radius to determine if the physicians are present in the room at the time logged to provide greater precision. The logged times, accurate to the second, were compared with physicians' handwritten times, showing automatic recordings to be more precise. This real time automatic method will free the physician from extra cognitive load of manually recording data. This method for evaluation of performance is generic and can be used in any other setting outside the ED, and for purposes other than measuring physician time.